pyproject.toml

[build-system]
requires = [
    "maturin>=0.14.13,<0.15",
    "cffi",
]
build-backend = 'maturin'

[project]
name = "sourmash"
description = "tools for comparing biological sequences with k-mer sketches"
readme = "README.md"
version = "4.7.0"

authors = [
  { name="Luiz Irber", orcid="0000-0003-4371-9659" },
  { name="Mohamed Abuelanin", orcid="0000-0002-3419-4785" },
  { name="Harriet Alexander", orcid="0000-0003-1308-8008" },
  { name="Abhishek Anant", orcid="0000-0002-5751-2010" },
  { name="Keya Barve", orcid="0000-0003-3241-2117" },
  { name="Colton Baumler", orcid="0000-0002-5926-7792" },
  { name="Olga Botvinnik", orcid="0000-0003-4412-7970" },
  { name="Phillip Brooks", orcid="0000-0003-3987-244X" },
  { name="Peter Cock", orcid="0000-0001-9513-9993" },
  { name="Daniel Dsouza", orcid="0000-0001-7843-8596" },
  { name="Laurent Gautier", orcid="0000-0003-0638-3391" },
  { name="Tim Head", orcid="0000-0003-0931-3698" },
  { name="Mahmudur Rahman Hera", orcid="0000-0002-5992-9012" },
  { name="Hannah Eve Houts", orcid="0000-0002-7954-4793" },
  { name="Lisa K. Johnson", orcid="0000-0002-3600-7218" },
  { name="Fabian Klötzl", orcid="0000-0002-6930-0592" },
  { name="David Koslicki", orcid="0000-0002-0640-954X" },
  { name="Katrin Leinweber", orcid="0000-0001-5135-5758" },
  { name="Marisa Lim", orcid="0000-0003-2097-8818" },
  { name="Ricky Lim", orcid="0000-0003-1313-7076" },
  { name="Ivan Ogasawara", orcid="0000-0001-5049-4289" },
  { name="N. Tessa Pierce", orcid="0000-0002-2942-5331" },
  { name="Taylor Reiter", orcid="0000-0002-7388-421X" },
  { name="Camille Scott", orcid="0000-0001-8822-8779" },
  { name="Andreas Sjödin", orcid="0000-0001-5350-4219" },
  { name="Connor T. Skennerton", orcid="0000-0003-1320-4873" },
  { name="Jason Stajich", orcid="0000-0002-7591-0020" },
  { name="Daniel Standage", orcid="0000-0003-0342-8531" },
  { name="S. Joshua Swamidass", orcid="0000-0003-2191-0778" },
  { name="Connor Tiffany", orcid="0000-0001-8188-7720" },
  { name="Pranathi Vemuri", orcid="0000-0002-5748-9594"},
  { name="Erik Young", orcid="0000-0002-9195-9801" },
  { name="Nick H", orcid="0000-0002-1685-302X" },
  { name="C. Titus Brown", orcid="0000-0001-6001-2677" },
]

maintainers = [
  { name="Luiz Irber", email="luiz@sourmash.bio", orcid="0000-0003-4371-9659" },
  { name="C. Titus Brown", email="titus@idyll.org", orcid="0000-0001-6001-2677" },
]

classifiers = [
  "Development Status :: 5 - Production/Stable",
  "Environment :: Console",
  "Environment :: MacOS X",
  "Intended Audience :: Science/Research",
  "License :: OSI Approved :: BSD License",
  "Natural Language :: English",
  "Operating System :: POSIX :: Linux",
  "Operating System :: MacOS :: MacOS X",
  "Programming Language :: Rust",
  "Programming Language :: Python :: 3.8",
  "Programming Language :: Python :: 3.9",
  "Programming Language :: Python :: 3.10",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
]

dependencies = [
  "screed>=1.1.2,<2",
  "cffi>=1.14.0",
  "numpy",
  "matplotlib",
  "scipy",
  "deprecation>=2.0.6",
  "cachetools>=4,<6",
  "bitstring>=3.1.9,<5",
  "importlib_metadata>=3.6;python_version<'3.10'"
]

requires-python = ">=3.8"

[metadata]
license = { text = "BSD 3-Clause License" }

[project.urls]
"Homepage" = "https://sourmash.bio/"
"Documentation" = "https://sourmash.readthedocs.io"
"CI" = "https://github.com/sourmash-bio/sourmash/actions"
"Source" = "https://github.com/sourmash-bio/sourmash"
"Tracker" = "https://github.com/sourmash-bio/sourmash/issues"

[project.scripts]
"sourmash" = "sourmash.__main__:main"

[project.optional-dependencies]
test = [
  "pytest>=6.2.4,<7.3.0",
  "pytest-cov>=2.12,<5.0",
  "pytest-xdist",
  "pyyaml>=6,<7",
  "recommonmark",
  "hypothesis",
  "build",
]
demo = [
  "jupyter",
  "jupyter_client",
  "ipython",
]
doc = [
  "sphinx>=4.4.0,<7",
  "myst-parser==1.0.0",
  "Jinja2==3.1.2",
  "alabaster",
  "sphinxcontrib-napoleon",
  "nbsphinx",
  "ipython",
  "docutils>=0.17.1,<0.20",
]
storage = [
  "ipfshttpclient>=0.4.13",
  "redis",
]
# hmm, I think this is a hack, but it works...
# https://github.com/pypa/pip/issues/10393#issuecomment-941885429
all = ["sourmash[test,demo,doc,storage]"]

[tool.maturin]
python-source = "src"
manifest-path = "src/core/Cargo.toml"
bindings = "cffi"
include = [
  { path = "include/sourmash.h", format = ["sdist","wheel"] },
  { path = "requirements.txt", format = ["sdist"] },
  { path = "Cargo.*", format = ["sdist"] },
  { path = "tests/**/*", format = ["sdist"] },
  { path = "CITATION.cff", format = ["sdist", "wheel"] },
  { path = "LICENSE", format = ["sdist"] },
]
exclude = [
  { path = "**/__pycache__/*", format = ["sdist", "wheel"] },
]
features = ["maturin"]
locked = true

[tool.isort]
known_third_party = ["deprecation", "hypothesis", "mmh3", "numpy", "pytest", "screed", "sourmash_tst_utils"]
multi_line_output = 3 
include_trailing_comma = true
force_grid_wrap = 0
line_length = 88
known_first_party = ["sourmash"]

[tool.cibuildwheel]
build = "cp39-*"
skip = "*-win32 *-manylinux_i686 *-musllinux_ppc64le *-musllinux_s390x"
before-build = "source .ci/install_cargo.sh"
environment = { PATH="$HOME/.cargo/bin:$PATH" }
build-verbosity = 3

[tool.pytest.ini_options]
addopts = "--doctest-glob='doc/*.md' -n4"
norecursedirs = [
  "utils",
  "build",
  "buildenv",
  ".tox",
  ".asv",
  ".eggs",
]
testpaths = [
  "tests",
  "doc",
]