# 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)
import glob

from spack.package import *


class Raxml(Package):
    """RAxML (Randomized Axelerated Maximum Likelihood) is a program for
    sequential and parallel Maximum Likelihood based inference of large
    phylogenetic trees.
    """

    homepage = "https://sco.h-its.org/exelixis/web/software/raxml"
    url = "https://github.com/stamatak/standard-RAxML/archive/v8.2.12.tar.gz"

    license("GPL-3.0-or-later")

    version("8.2.12", sha256="338f81b52b54e16090e193daf36c1d4baa9b902705cfdc7f4497e3e09718533b")
    version("8.2.11", sha256="08cda74bf61b90eb09c229e39b1121c6d95caf182708e8745bd69d02848574d7")

    depends_on("c", type="build")  # generated

    variant("mpi", default=True, description="Enable MPI parallel support")
    variant("pthreads", default=False, description="Enable pthreads version")

    depends_on("mpi", when="+mpi")

    patch("nox86.patch")

    # Compiles with either GCC or ICC.
    conflicts("%cce")
    conflicts("%apple-clang")
    conflicts("%clang")
    conflicts("%nag")
    conflicts("%xl")
    conflicts("%xl_r")

    # can't build multiple binaries in parallel without things breaking
    parallel = False

    def install(self, spec, prefix):
        mkdirp(prefix.bin)
        files = glob.iglob("Makefile.*")
        for file in files:
            makefile = FileFilter(file)
            makefile.filter("gcc", spack_cc)
            if spec.satisfies("+mpi"):
                makefile.filter("mpicc", self.spec["mpi"].mpicc)

        if spec.target.family == "x86_64":
            if spec.satisfies("+mpi +pthreads") and "avx" in spec.target:
                make("-f", "Makefile.AVX.HYBRID.gcc")
                install("raxmlHPC-HYBRID-AVX", prefix.bin)

            if spec.satisfies("+mpi +pthreads") and "sse3" in spec.target:
                make("-f", "Makefile.SSE3.HYBRID.gcc")
                install("raxmlHPC-HYBRID-SSE3", prefix.bin)

            if spec.satisfies("+mpi +pthreads"):
                make("-f", "Makefile.HYBRID.gcc")
                install("raxmlHPC-HYBRID", prefix.bin)

            if spec.satisfies("+mpi") and "avx" in spec.target:
                make("-f", "Makefile.AVX.MPI.gcc")
                install("raxmlHPC-MPI-AVX", prefix.bin)

            if spec.satisfies("+mpi") and "sse3" in spec.target:
                make("-f", "Makefile.SSE3.MPI.gcc")
                install("raxmlHPC-MPI-SSE3", prefix.bin)

            if spec.satisfies("+mpi"):
                make("-f", "Makefile.MPI.gcc")
                install("raxmlHPC-MPI", prefix.bin)

            if spec.satisfies("+pthreads") and "avx" in spec.target:
                make("-f", "Makefile.AVX.PTHREADS.gcc")
                install("raxmlHPC-PTHREADS-AVX", prefix.bin)

            if spec.satisfies("+pthreads") and "sse3" in spec.target:
                make("-f", "Makefile.SSE3.PTHREADS.gcc")
                install("raxmlHPC-PTHREADS-SSE3", prefix.bin)

            if spec.satisfies("+pthreads"):
                make("-f", "Makefile.PTHREADS.gcc")
                install("raxmlHPC-PTHREADS", prefix.bin)

            if "sse3" in spec.target:
                make("-f", "Makefile.SSE3.gcc")
                install("raxmlHPC-SSE3", prefix.bin)

            if "avx" in spec.target:
                make("-f", "Makefile.AVX.gcc")
                install("raxmlHPC-AVX", prefix.bin)

            make("-f", "Makefile.gcc")
            install("raxmlHPC", prefix.bin)
        else:
            if spec.satisfies("+mpi +pthreads"):
                make("-f", "Makefile.HYBRID.nox86.gcc")
                install("raxmlHPC-HYBRID", prefix.bin)

            if spec.satisfies("+mpi"):
                make("-f", "Makefile.MPI.nox86.gcc")
                install("raxmlHPC-MPI", prefix.bin)

            if spec.satisfies("+pthreads"):
                make("-f", "Makefile.PTHREADS.nox86.gcc")
                install("raxmlHPC-PTHREADS", prefix.bin)

            make("-f", "Makefile.nox86.gcc")
            install("raxmlHPC", prefix.bin)
