pyproject.toml

[build-system]
# wnetalign's extension shares nanobind-registered types (e.g. NetworkSimplexConfig,
# CVectorDistributionFloat*) with the wnet and pylmcf extensions. That used to
# require pinning all three to one nanobind internals-ABI version by hand, with a
# mismatch showing up as "ImportError: std::bad_cast" at import. Since nanobind 3
# these extensions are built in split mode and share a single `nanobind_backend`
# module, which gives them full mutual visibility of each other's type bindings
# regardless of which nanobind each was compiled against. Hence no upper bound.
# scikit-build-core>=1.0: the [[tool.dynamic-metadata]] table below is the 0.3
# spec, which older backends do not read. They would not fail -- they would
# ignore it, leaving `dynamic = ["dependencies"]` unresolved and shipping a
# wheel that declares no dependencies at all.
requires = ["scikit-build-core>=1.0", "nanobind>=3.0.1", "pylmcf>=1.2.1", "wnet>=1.3.0"]
build-backend = "scikit_build_core.build"

[project]
name = "wnetalign"
version = "1.1.0"
description = "Python implementation of spectral alignment using Wasserstein metric"
# Resolved per-build by _wnetalign_metadata.py: nanobind-backend is required only
# by a split-mode build, and no PEP 508 marker can see which mode CMake picked
# (in particular none can say "not a free-threaded interpreter").
dynamic = ["dependencies"]
authors = [{ name="Michał Startek", email="michal.startek@mimuw.edu.pl" }]
maintainers = [{ name="Michał Startek", email="michal.startek@mimuw.edu.pl" }]
readme = "README.md"
license = "MIT"
license-files = ["LICENCE"]
classifiers = [
    "Programming Language :: Python :: 3",
    "Topic :: Scientific/Engineering :: Mathematics",
    "Topic :: Software Development :: Libraries :: Python Modules",
    "Development Status :: 5 - Production/Stable",
]
requires-python = ">=3.10"

[project.urls]
"Homepage" = "https://github.com/michalsta/wnetalign"
"Repository" = "https://github.com/michalsta/wnetalign.git"

[project.optional-dependencies]
extras = ["pyopenms"]
pytest = ["pytest", "pandas", "numpy"]

[tool.pytest.ini_options]
testpaths = ["tests"]

[tool.scikit-build]
# Split-mode extensions are stable-ABI builds. Declaring the target here gets the
# wheel an `abi3` tag, and nanobind reads it back as SKBUILD_SABI_VERSION to set
# the stable ABI floor, so the two can never drift apart. One wheel per platform
# then covers every Python from 3.10 up. Ignored automatically on PyPy and on
# free-threaded interpreters, which is exactly when CMake falls back to a linked
# build.
wheel.py-api = "cp310"

# A free-threaded interpreter has no classic Stable ABI, so the cp310 request
# above is simply ignored there and the build would fall out as a version-locked
# cp315t wheel. abi3t (PEP 803, 3.15+) is the free-threaded equivalent; ask for
# it explicitly so that lane gets its own portable wheel. Deliberately *not*
# "cp310.cp315t", which would emit a combined cp315-abi3.abi3t tag that a
# GIL-enabled 3.15 would also match, quietly outranking the cp310-abi3 wheel.
[[tool.scikit-build.overrides]]
if.abi-flags = "t"
wheel.py-api = "cp315t"

[tool.scikit-build.sdist]
# Exclude-list, matching pylmcf/wnet/wnetdeconv. This used to be an allowlist
# (`exclude = ["**/*"]` plus an `include` of /src/**), which current
# scikit-build-core resolves in favour of the exclude: the resulting sdist held
# only README/LICENCE/pyproject/CMakeLists and could not be built at all.
exclude = [
    ".github/",
    ".gitignore",
    ".pytest_cache/",
    "tests/",
    "tests_cpp/",
    "tutorials/",
    "publication/",
    "runtime/",
    "reinstall.sh",
    "CLAUDE.md",
    "**/__pycache__/",
]

# scikit-build-core reads dynamic-metadata providers from its own namespace,
# keyed by the field they supply; a top-level [[tool.dynamic-metadata]] table is
# silently ignored, which leaves `dynamic = ["dependencies"]` resolving to
# nothing at all and ships a wheel that declares no dependencies whatsoever.
# The standard top-level dynamic-metadata table (0.3 spec). The previous
# [tool.scikit-build.metadata.dependencies] form was deprecated in
# scikit-build-core 1.0 and warns on every build; the two cannot be combined.
# The inline {path, module} value is how a local, in-project provider is named --
# a bare import string here would be looked up in the dynamic_metadata.provider
# entry-point group instead, and not found. _wnetalign_metadata.py is kept in the
# sdist for exactly this reason.
[[tool.dynamic-metadata]]
provider = { path = ".", module = "_wnetalign_metadata" }