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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 import *
from spack.pkg.builtin.boost import Boost
class Revbayes(CMakePackage):
"""Bayesian phylogenetic inference using probabilistic graphical models
and an interpreted language."""
homepage = "https://revbayes.github.io"
url = "https://github.com/revbayes/revbayes/archive/1.1.0.tar.gz"
git = "https://github.com/revbayes/revbayes.git"
version('develop', branch='development')
version('1.1.1', sha256='d61293fceac817d8203ed1e828661d76c73fa16bf04458a50a37057e99fd40c0')
version('1.1.0', sha256='a9f35178d8289d0dd32c9d936f6384f260e8e81e7b80a5155169064a24666012')
version('1.0.13', sha256='e85e2e1fe182fe9f504900150d936a06d252a362c591b9d3d8272dd085aa85d9')
version('1.0.12', sha256='80c926bb6b37288d02e36e07b44e4663841cd1fe541e2cc0b0e44c89ca929759')
version('1.0.11', sha256='03052194baa220dde7e622a739f09f34393f67ea00a0b163b409d313d7fc7c02')
version('1.0.10', sha256='6a3cf303e7224b0b32637bd8e2c3c2cf2621f5dbe599cd74ce4b0c215d0fcd2d')
variant('mpi', default=True, description='Enable MPI parallel support')
# TODO: replace this with an explicit list of components of Boost,
# for instance depends_on('boost +filesystem')
# See https://github.com/spack/spack/pull/22303 for reference
depends_on(Boost.with_default_variants)
depends_on('mpi', when='+mpi')
conflicts('%gcc@7.1.0:', when='@:1.0.12')
def url_for_version(self, version):
if version > Version('1.0.13'):
return 'https://github.com/revbayes/revbayes/archive/{0}.tar.gz'.format(version)
else:
return 'https://github.com/revbayes/revbayes.archive/archive/v{0}.tar.gz'.format(version)
@property
def root_cmakelists_dir(self):
if self.spec.version > Version('1.0.13'):
return 'src'
else:
return 'projects/cmake/build'
@when('@1.1.0:')
def cmake_args(self):
args = []
if '+mpi' in self.spec:
args.extend([
self.define('MPI', 'ON'),
self.define('RB_EXEC_NAME', 'rb-mpi'),
])
return args
@run_before('cmake')
def regenerate(self):
with working_dir(join_path('projects', 'cmake')):
mkdirp('build')
if self.spec.version > Version('1.0.13'):
generate_version = Executable('./generate_version_number.sh')
generate_version()
dest = join_path('..', '..', 'src', 'revlanguage', 'utils')
install('GitVersion.cpp', dest)
else:
edit = FileFilter('regenerate.sh')
edit.filter('boost="true"', 'boost="false"')
if '+mpi' in self.spec:
edit.filter('mpi="false"', 'mpi="true"')
regenerate = Executable('./regenerate.sh')
regenerate()
def install(self, spec, prefix):
mkdirp(prefix.bin)
if '+mpi' in spec:
install_path = join_path(self.build_directory, '..', 'rb-mpi')
install(install_path, prefix.bin)
else:
install_path = join_path(self.build_directory, '..', 'rb')
install(install_path, prefix.bin)
@when('@1.0.12:1.0.13')
def install(self, spec, prefix):
mkdirp(prefix.bin)
install_path = join_path(self.build_directory, '..', 'rb')
install(install_path, prefix.bin)
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