old_contents: # Copyright 2013-2019 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 *
  
  
  class Mrbayes(AutotoolsPackage):
      """MrBayes is a program for Bayesian inference and model choice across a
         wide range of phylogenetic and evolutionary models. MrBayes uses Markov
         chain Monte Carlo (MCMC) methods to estimate the posterior distribution
         of model parameters."""
  
      homepage = "http://mrbayes.sourceforge.net"
      git      = "https://github.com/NBISweden/MrBayes.git"
  
      version('2017-11-22', commit='8a9adb11bcc538cb95d91d57568dff383f924503')
  
      variant('mpi', default=True, description='Enable MPI parallel support')
      variant('beagle', default=True, description='Enable BEAGLE library for speed benefits')
      variant('sse', default=True, description='Enable SSE in order to substantially speed up execution')
  
      depends_on('autoconf', type='build')
      depends_on('automake', type='build')
      depends_on('libtool',  type='build')
      depends_on('m4',       type='build')
  
      depends_on('libbeagle', when='+beagle')
      depends_on('mpi', when='+mpi')
  
      def configure_args(self):
          args = []
          if '~beagle' in self.spec:
              args.append('--with-beagle=no')
          else:
              args.append('--with-beagle=%s' % self.spec['libbeagle'].prefix)
          if '~sse' in self.spec:
              args.append('--enable-sse=no')
          else:
              args.append('--enable-sse=yes')
          if '~mpi' in self.spec:
              args.append('--enable-mpi=no')
          else:
              args.append('--enable-mpi=yes')
          return args
  
      def install(self, spec, prefix):
          mkdirp(prefix.bin)
          with working_dir('src'):
              install('mb', prefix.bin)
  
new_contents: # Copyright 2013-2019 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 *
  
  
  class Mrbayes(AutotoolsPackage):
      """MrBayes is a program for Bayesian inference and model choice across a
         wide range of phylogenetic and evolutionary models. MrBayes uses Markov
         chain Monte Carlo (MCMC) methods to estimate the posterior distribution
         of model parameters."""
  
      homepage = "http://mrbayes.sourceforge.net"
      url      = "https://github.com/NBISweden/MrBayes/releases/download/v3.2.7a/mrbayes-3.2.7a.tar.gz"
  
      version('3.2.7a', sha256='1a4670be84e6b968d59382328294db4c8ceb73e0c19c702265deec6f2177815c')
      version('3.2.7',  sha256='39d9eb269969b501268d5c27f77687c6eaa2c71ccf15c724e6f330fc405f24b9')
  
      variant('mpi', default=True, description='Enable MPI parallel support')
      variant('beagle', default=True, description='Enable BEAGLE library for speed benefits')
      variant('readline', default=False, description='Enable readline library, not recommended with MPI')
  
      depends_on('libbeagle', when='+beagle')
      depends_on('mpi', when='+mpi')
      depends_on('readline', when='+readline')
  
      def configure_args(self):
          args = []
          if '~beagle' in self.spec:
              args.append('--with-beagle=no')
          else:
              args.append('--with-beagle=%s' % self.spec['libbeagle'].prefix)
          if '+readline' in self.spec:
              args.append('--with-readline=yes')
          else:
              args.append('--with-readline=no')
          if '~mpi' in self.spec:
              args.append('--with-mpi=no')
          else:
              args.append('--with-mpi=yes')
          return args
  
      def install(self, spec, prefix):
          mkdirp(prefix.bin)
          with working_dir('src'):
              install('mb', prefix.bin)
  
subject: Update MrBayes to 3.2.7a and correct MPI variants (#13929)