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# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class Sourmash(PythonPackage):
"""Sourmash: Quickly search, compare, and analyze genomic and metagenomic data sets with
k-mer sketches."""
homepage = "https://sourmash.bio/"
pypi = "sourmash/sourmash-4.8.2.tar.gz"
version("4.8.2", sha256="e0df78032e53ed88977445933ba3481dd10c7d3bd26d019511a6a4e6d7518475")
depends_on("python@3.8:", type=("build", "run"))
# build-only
depends_on("py-maturin@0.14.13:0.14", type="build")
depends_on("rust", type="build")
# general
depends_on("py-screed@1.1.2:1", type=("build", "run"))
depends_on("py-cffi@1.14.0:", type=("build", "run"))
depends_on("py-numpy", type=("build", "run"))
depends_on("py-matplotlib", type=("build", "run"))
depends_on("py-scipy", type=("build", "run"))
depends_on("py-deprecation@2.0.6:", type=("build", "run"))
depends_on("py-cachetools@4:5", type=("build", "run"))
depends_on("py-bitstring@3.1.9:4", type=("build", "run"))
depends_on("py-importlib_metadata@3.6:", when="^python@:3.9", type=("build", "run"))
def install(self, spec, prefix):
# build rust libs
cargo = Executable("cargo")
cargo("build", "--release")
# install python package
args = std_pip_args + ["--prefix=" + prefix, "."]
pip(*args)
# move sourmash.so into expected place
site_packages = join_path(python_platlib, "sourmash")
lib_ext = "dylib" if spec.platform == "Darwin" else "so"
install(
join_path("target", "release", "libsourmash.{}".format(lib_ext)),
join_path(site_packages, "_lowlevel__lib.so"),
)
# patch invalid read mode
filter_file(r"'(.*)'\), 130\)", r"'\1'))", join_path(site_packages, "_lowlevel.py"))
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