pyproject.toml

[build-system]
requires = ["setuptools>=64", "wheel", "setuptools_scm"]
build-backend = "setuptools.build_meta"

[project]
name = "singlem"
description = "Novelty-inclusive microbial community profiling of shotgun metagenomes"
readme = "README.md"
requires-python = ">=3.7"
license = "GPL-3.0-or-later"
authors = [{ name = "Ben Woodcroft" }]
keywords = ["metagenomics", "bioinformatics"]
classifiers = [
    "Development Status :: 4 - Beta",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Programming Language :: Python :: 3"
]
dynamic = ["version", "dependencies"]

[project.urls]
Homepage = "https://github.com/wwood/SingleM"

[project.scripts]
singlem = "singlem.main:main"
lyrebird = "singlem.lyrebird:main"

[tool.setuptools]
packages = ["singlem", "singlem.biolib_lite"]
include-package-data = true

[tool.setuptools.dynamic]
dependencies = { file = ["admin/requirements.txt"] }

[tool.setuptools_scm]
version_file = "singlem/version.py"
# Otherwise the push to pypi will fail on GitHub actions, because the version is malformed.
version_scheme = "only-version"
local_scheme = "no-local-version"

[tool.uv.sources]
# Use local editable install instead of PyPI, avoiding strict pins from published package
singlem = { workspace = true }