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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 Migrate(AutotoolsPackage):
"""Migrate estimates effective population sizes and past migration rates
between n population assuming a migration matrix model with asymmetric
migration rates and different subpopulation sizes"""
homepage = "https://popgen.sc.fsu.edu/"
url = "https://popgen.sc.fsu.edu/currentversions/migrate-3.6.11.src.tar.gz"
license("Unlicense")
version("3.6.11", sha256="a9ba06a4e995a45b8d04037f5f2da23e1fe64a2f3565189bdd50c62c6fe01fb8")
variant("mpi", default=False, description="Build MPI binaries")
depends_on("autoconf", type="build")
depends_on("automake", type="build")
depends_on("libtool", type="build")
depends_on("m4", type="build")
depends_on("zlib-api", type="link")
depends_on("openmpi", type=("build", "link", "run"), when="+mpi")
configure_directory = "src"
def configure_args(self):
return ["--with-zlib=system"]
def build(self, spec, prefix):
with working_dir("src"):
# this software is written with parts both in C and C++.
# it tries to link using gcc which causes problems, so this package
# explicitly links with g++ (CXX) instead.
# spack's FileFilter/filter_file only work per-line (see docs),
# so the package uses a custom filter by replacing substrings
# in the Makefile.
mfc = ""
with open("Makefile") as m:
mfc = mfc_old = m.read()
# replace linking step
mfc = mfc.replace(
"$(NAME): $(PRODUCT_DEPENDS)\n\t$(CC)", "$(NAME): $(PRODUCT_DEPENDS)\n\t$(CXX)"
)
mfc = mfc.replace(
"$(MPINAME): $(PRODUCT_DEPENDS)\n\t$(CC)",
"$(MPINAME): $(PRODUCT_DEPENDS)\n\t$(CXX)",
)
# make sure the replace worked
if mfc == mfc_old:
raise InstallError("Failed to update linker command")
# don't try to install MPI binaries that aren't there
if "+mpi" not in spec:
line = "$(INSTALL) $(IFLAGS) $(MPINAME) $(INSTALLDIR)"
mfc = mfc.replace(line, "")
# write modified makefile back
with open("Makefile", "w") as m:
m.write(mfc)
make()
if "+mpi" in spec:
make("mpis")
def install(self, spec, prefix):
mkdirp(prefix.man)
with working_dir("src"):
make("install")
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