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# Copyright 2013-2023 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 PyTopiaryAsr(PythonPackage):
"""Python framework for doing ancestral sequence reconstruction."""
homepage = "https://github.com/harmslab/topiary"
url = "https://github.com/harmslab/topiary/archive/refs/tags/v0.9.9.tar.gz"
git = "https://github.com/harmslab/topiary.git"
maintainers("snehring")
license("MIT")
version("main", branch="main")
version("0.9.9", sha256="5601fba92e7add33a3732482426b2c7ef46b0fccc4a4ea11357537e1b937903c")
depends_on("python@3.8:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-biopython", type=("build", "run"))
depends_on("py-numpy@:1.21", type=("build", "run"), when="@0.9.9")
depends_on("py-numpy", type=("build", "run"), when="@main")
depends_on("py-pandas", type=("build", "run"))
depends_on("py-matplotlib", type=("build", "run"))
depends_on("py-ete3", type=("build", "run"))
depends_on("py-toytree", type=("build", "run"))
depends_on("py-dendropy", type=("build", "run"))
depends_on("py-pastml", type=("build", "run"))
depends_on("py-openpyxl", type=("build", "run"))
depends_on("py-opentree", type=("build", "run"))
depends_on("py-tqdm", type=("build", "run"))
depends_on("py-xlrd", type=("build", "run"))
# while undocumented, this requires mpi4py to run
depends_on("py-mpi4py", type=("build", "run"))
# runtime deps from https://topiary-asr.readthedocs.io/en/latest/installation.html#required-libraries
depends_on("blast-plus", type="run")
depends_on("muscle5@5.0:", type="run")
depends_on("generax@2.0:+mpi", type="run")
depends_on("raxml-ng@1.1:", type="run")
depends_on("mpi", type="run")
depends_on("openmpi+legacylaunchers", type="run", when="^openmpi schedulers=slurm")
conflicts("^mpich")
def patch(self):
if self.spec.satisfies("^raxml-ng+mpi"):
filter_file(
r"RAXML_BINARY\s*=\s*\"raxml-ng\"$",
'RAXML_BINARY = "raxml-ng-mpi"',
join_path("topiary", "raxml", "_raxml.py"),
)
filter_file(
r"binary\s*=\s*\"raxml-ng\"",
'binary = "raxml-ng-mpi"',
join_path("topiary", "_private", "installed.py"),
)
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