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# Copyright 2013-2022 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 PyCogent(PythonPackage):
"""A toolkit for statistical analysis of biological sequences."""
homepage = "https://github.com/Magdoll/Cogent/wiki/Installing-Cogent"
pypi = "cogent/cogent-1.9.tar.gz"
version("1.9", sha256="57d8c58e0273ffe4f2b907874f9b49dadfd0600f5507b7666369f4e44d56ce14")
version(
"1.5.3",
url="https://pypi.io/packages/source/c/cogent/cogent-1.5.3.tgz",
sha256="1215ac219070b7b2207b0b47b4388510f3e30ccd88160aa9f02f25d24bcbcd95",
)
variant("matplotlib", default=False, description="graphs related to codon usage")
variant("mpi", default=False, description="MPI required for parallel computation.")
variant("mysql", default=False, description="Required for the Ensembl querying code.")
depends_on("py-setuptools", type=("build"), when="@1.9")
depends_on("python@2.6:2", type=("build", "run"))
depends_on("py-numpy@1.3:", type=("build", "run"))
depends_on("zlib")
depends_on("py-matplotlib", when="+matplotlib", type=("build", "run"))
depends_on("py-mpi4py", when="+mpi", type=("build", "run"))
depends_on("py-sqlalchemy", when="+mysql", type=("build", "run"))
depends_on("py-pymysql", when="+mysql", type=("build", "run"))
depends_on("py-cython@0.17.1:", type="build")
def setup_build_environment(self, env):
env.set("DONT_USE_PYREX", "1")
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