old_contents: # Copyright 2013-2021 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 Dssp(AutotoolsPackage):
      """'mkdssp' utility. (dictionary of protein secondary structure)"""
  
      homepage = "https://github.com/cmbi/dssp"
      url      = "https://github.com/cmbi/dssp/archive/3.1.4.tar.gz"
  
      version('3.1.4', sha256='496282b4b5defc55d111190ab9f1b615a9574a2f090e7cf5444521c747b272d4')
      version('2.3.0', sha256='4c95976d86dc64949cb0807fbd58c7bee5393df0001999405863dc90f05846c6')
  
      depends_on('autoconf', type='build')
      depends_on('automake', type='build')
      depends_on('libtool',  type='build')
      depends_on('m4',       type='build')
      depends_on('boost@1.48:')
  
      # pdb data download.
      # 1ALK.pdb - PDB (protein data bank) : https://www.rcsb.org/
      resource(
          name="pdb_data",
          url="https://files.rcsb.org/download/1ALK.pdb",
          sha256="99f4cd7ab63b35d64eacc85dc1491af5a03a1a0a89f2c9aadfb705c591b4b6c9",
          expand=False,
          placement='pdb'
      )
  
      def configure_args(self):
          args = [
              "--with-boost=%s" % self.spec['boost'].prefix]
          return args
  
      @run_after('configure')
      def edit(self):
          makefile = FileFilter(join_path(self.stage.source_path, 'Makefile'))
          makefile.filter('.*-Werror .*', '                    -Wno-error \\')
  
      @run_after('install')
      def cache_test_sources(self):
          self.cache_extra_test_sources('pdb')
  
      def test(self):
          pdb_path  = join_path(self.install_test_root, 'pdb')
          self.run_test('mkdssp', options=['1ALK.pdb', '1alk.dssp'], work_dir=pdb_path)
  
new_contents: # Copyright 2013-2021 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 Dssp(AutotoolsPackage):
      """'mkdssp' utility. (dictionary of protein secondary structure)"""
  
      homepage = "https://github.com/cmbi/dssp"
      url      = "https://github.com/cmbi/dssp/archive/3.1.4.tar.gz"
  
      version('3.1.4', sha256='496282b4b5defc55d111190ab9f1b615a9574a2f090e7cf5444521c747b272d4')
      version('2.3.0', sha256='4c95976d86dc64949cb0807fbd58c7bee5393df0001999405863dc90f05846c6')
  
      depends_on('autoconf', type='build')
      depends_on('automake', type='build')
      depends_on('libtool',  type='build')
      depends_on('m4',       type='build')
      depends_on('boost@1.48:')
  
      # pdb data download.
      # 1ALK.pdb - PDB (protein data bank) : https://www.rcsb.org/
      resource(
          name="pdb_data",
          url="https://files.rcsb.org/download/1ALK.pdb",
          sha256="99f4cd7ab63b35d64eacc85dc1491af5a03a1a0a89f2c9aadfb705c591b4b6c9",
          expand=False,
          placement='pdb'
      )
  
      def configure_args(self):
          args = [
              "--with-boost=%s" % self.spec['boost'].prefix]
          return args
  
      @run_after('configure')
      def edit(self):
          makefile = FileFilter(join_path(self.stage.source_path, 'Makefile'))
          makefile.filter('.*-Werror .*', '                    -Wno-error \\')
  
      @run_after('install')
      def cache_test_sources(self):
          """Save off the pdb sources for stand-alone testing."""
          self.cache_extra_test_sources('pdb')
  
      def test(self):
          """Perform stand-alone/smoke test on installed package."""
          pdb_path  = join_path(self.test_suite.current_test_cache_dir, 'pdb')
          self.run_test('mkdssp', options=['1ALK.pdb', '1alk.dssp'],
                        purpose='test: calculating structure for example',
                        installed=True,
                        work_dir=pdb_path)
  
subject: Update stand-alone tests to use test stage work directory (#24112)