setup.py

from pathlib import Path
import tomllib

from setuptools import find_namespace_packages, find_packages, setup
from pybind11.setup_helpers import Pybind11Extension, build_ext


ROOT = Path(__file__).resolve().parent


def sibling_dependencies(sibling: str, *, extra: str) -> list[str]:
    """Read a sibling's extra without installing its core distribution."""
    sibling_path = ROOT.parent / sibling
    pyproject = sibling_path / "pyproject.toml"
    if not pyproject.is_file():
        return [f"{sibling}[{extra}]"]
    with pyproject.open("rb") as handle:
        project = tomllib.load(handle)["project"]
    dependencies = list(project.get("dependencies", []))
    dependencies.extend(project.get("optional-dependencies", {}).get(extra, []))
    # Lasagna imports only vesuvius.models. The bootstrap owns the machine-
    # specific torch build; VC and cuCIM are unrelated to this model builder.
    excluded = ("volume-cartographer", "torch", "cucim-cu13")
    return [
        dependency
        for dependency in dependencies
        if not dependency.startswith(excluded)
    ]

# Lasagna predates its packaging metadata and its modules intentionally use
# top-level imports (for example ``import fit_data``).  Install those modules
# as-is so editable and regular installs behave like running from this folder.
py_modules = sorted(
    path.stem
    for path in ROOT.glob("*.py")
    if path.name != "setup.py"
)
packages = find_packages(
    include=("lasagna3d", "lasagna3d.*", "snap_surf", "snap_surf.*", "scripts")
)
# Also expose the legacy root modules through their canonical ``lasagna.*``
# imports.  They remain top-level ``py_modules`` for backwards compatibility.
packages.append("lasagna")
# Preserve the programmatic import already used by callers and tests while the
# legacy internal imports continue to use the top-level ``scripts`` package.
packages.append("lasagna.scripts")
packages.append("lasagna.manager")

# Managed Fiber inference is part of the supported Lasagna runtime.  Package
# the sibling source directly so both editable installs and wheels made from
# the monorepo work without an ambient PYTHONPATH.  ``neural_tracing`` is a
# namespace package, hence find_namespace_packages rather than find_packages.
VESUVIUS_SOURCE = ROOT.parent / "vesuvius" / "src"
if not VESUVIUS_SOURCE.is_dir():
    raise RuntimeError(
        "the Lasagna build requires the sibling vesuvius/src tree; "
        "build from the villa monorepo checkout"
    )
packages.extend(find_namespace_packages(
    where=str(VESUVIUS_SOURCE),
    include=("vesuvius", "vesuvius.*", "vc3d_fiber_format", "vc3d_fiber_format.*"),
))

fit_service_requires = [
    "numpy>=1.24",
    "opencv-python-headless>=4.8",
    "scikit-image>=0.21",
    "scipy>=1.10",
    # snap_surf fixtures store N-D tensors with its shaped metadata.
    "tifffile>=2023.7.10",
    "torch>=2.1",
    # Monorepo-only: surfaces and fit artifacts are exchanged through the object
    # store; scripts/bootstrap_venv.py installs the sibling vc_object_store.
    "vc-object-store",
    # Monorepo-only until published: Zarr, TIFF and S3.
    "vc-reader",
]
downloader_requires = ["vc-reader"]
preprocess_requires = [
    "numpy>=1.24",
    "opencv-python-headless>=4.8",
    "torch>=2.1",
    "threadpoolctl>=3.1",
    "vc-reader",
]
preprocess_3d_requires = [
    *preprocess_requires,
    *downloader_requires,
    "edt>=3.0",
    "numba>=0.58",
    "tensorboard>=2.14",
    *sibling_dependencies("vesuvius", extra="models"),
]
all_requires = sorted(set(
    fit_service_requires + downloader_requires + preprocess_3d_requires
))

ext_modules = [
    Pybind11Extension(
        "monotone_norm",
        ["monotone_norm.cpp"],
    ),
    Pybind11Extension(
        "accumulator_add",
        ["accumulator_add.cpp"],
        cxx_std=17,
    ),
]

setup(
    name="vesuvius-lasagna",
    version="0.0.1",
    description="Surface fitting and OME-Zarr preprocessing tools",
    long_description=(ROOT / "README.md").read_text(encoding="utf-8"),
    long_description_content_type="text/markdown",
    python_requires=">=3.14,<3.15",
    py_modules=py_modules,
    packages=packages,
    package_dir={
        "lasagna": ".",
        "lasagna.scripts": "scripts",
        "lasagna.manager": "manager",
        "vesuvius": "../vesuvius/src/vesuvius",
        "vc3d_fiber_format": "../vesuvius/src/vc3d_fiber_format",
    },
    package_data={"vesuvius": ["**/*.json", "**/*.yaml", "**/*.yml"]},
    install_requires=all_requires,
    ext_modules=ext_modules,
    cmdclass={"build_ext": build_ext},
    extras_require={
        "test": ["pytest>=7"],
        "qualzz": ["dynamic-network-architectures"],
    },
    entry_points={
        "console_scripts": [
            "lasagna-fit-service=fit_service:main",
            "lasagna-download=lasagna.scripts.download_omezarr:main",
            "lasagna-download-list=lasagna.scripts.download_volume_list:main",
            "lasagna-bootstrap=lasagna.scripts.bootstrap_venv:main",
            "lasagna-preprocess=preprocess_cos_omezarr:cli_main",
            "las_manager=lasagna.manager.cli:main",
            "lasagna-predict3d-holescan=predict3d_holescan:main",
        ],
    },
    zip_safe=False,
)