# 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 *
from spack.pkg.builtin.boost import Boost


class HybridLambda(AutotoolsPackage):
    """Hybrid-Lambda is a software package that can simulate gene trees
    within a rooted species network or a rooted species tree under the
    coalescent process.

    The main feature of this program is that users can
    choose to use the standard Kingman coalescent process, which produces
    bifurcating genealogies, or two other Lambda coalescent processes,
    which produce multifurcating genealogies. The other feature is that
    hybrid sim uses extended Newick formatted strings to make it easier to
    represent hybridization events between species."""

    homepage = "https://github.com/hybridLambda/hybrid-Lambda"
    git = "https://github.com/hybridLambda/hybrid-Lambda.git"

    version("develop", submodules=True)

    depends_on("autoconf", type="build")
    depends_on("automake", type="build")
    depends_on("libtool", type="build")
    depends_on("m4", type="build")

    # 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("cppunit", type="test")

    @run_after("configure")
    def change_install_option_in_makefile(self):
        with working_dir("src"):
            filter_file(r"INSTALL = /bin/install -c", "INSTALL = /bin/install -C", "Makefile")

    @on_package_attributes(run_tests=True)
    def setup_build_environment(self, env):
        # build testcases with cppunit
        env.prepend_path("LD_LIBRARY_PATH", self.spec["cppunit"].libs.directories[0])