49 lines
2.0 KiB
Python
49 lines
2.0 KiB
Python
# 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.build_systems.python import PythonPipBuilder
|
|
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
|
|
pip(*PythonPipBuilder.std_args(self), f"--prefix={prefix}", ".")
|
|
# 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"))
|