pyproject.toml

[build-system]
requires = ["scikit-build-core>=0.12", "nanobind>=2.5"]
build-backend = "scikit_build_core.build"

[project]
name = "seqtree"
version = "1.3.2"
description = "Fast fuzzy search over biological sequences (C++ core, Python bindings)"
readme = "README.md"
requires-python = ">=3.10"
license = { text = "GPL-3.0-or-later" }
authors = [{ name = "ISALGO laboratory", email = "mikhail.shugay@gmail.com" }]
keywords = ["sequence-search", "fuzzy-matching", "CDR3", "immunology", "bioinformatics", "trie"]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
    "Programming Language :: Python :: 3",
    "Programming Language :: C++",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = []

[project.optional-dependencies]
# biopython is the ORACLE for seqtree.pairwise (NW/SW) -- a test-only dependency.
# seqtree itself has no runtime dependencies and must never import it.
test = ["pytest>=7.4", "pytest-cov>=4.1", "biopython>=1.81"]
bench = ["huggingface_hub"]
docs = ["sphinx", "pydata-sphinx-theme"]
control = ["huggingface_hub"]  # only needed to download controls larger than the bundled subset
pmhc = ["huggingface_hub"]     # only needed to fetch the isalgo/pmhc_data epitope tables

[project.urls]
Homepage = "https://github.com/antigenomics/seqtree"
Repository = "https://github.com/antigenomics/seqtree"
Documentation = "https://antigenomics.github.io/seqtree/"

[tool.scikit-build]
wheel.packages = ["python/seqtree"]
cmake.build-type = "Release"
# Keep the sdist lean: ship only what builds the package. Anchor with a leading "/".
sdist.exclude = [
    "/bench", "/tests", "/docs", "/.github", "/setup.sh", "/build", "/appendix", "/examples",
    # Local agent config: machine-specific absolute paths and unrelated repo names.
    "/.claude", "/CLAUDE.md", "/AGENTS.md", "/ROADMAP.md", "/SOURCES.md", "/skills",
    "/tmp", "/add_bindings.py", "/add_native.py", "/appendix/immunogenicity_hooks.md",
]
editable.rebuild = false

[tool.scikit-build.cmake.define]
SEQTREE_PYTHON = "ON"