Merge branch 'features/cantera' of https://github.com/adamjstewart/spack into adamjstewart-features/cantera

lib/spack/spack/build_environment.py

@@ -63,7 +63,7 @@
 import spack
 from spack.environment import EnvironmentModifications, validate
 from spack.util.environment import *
-from spack.util.executable import Executable, which
+from spack.util.executable import Executable
 
 #
 # This can be set by the user to globally disable parallel builds.
@@ -130,8 +130,13 @@ def load_module(mod):
     text = modulecmd('show', mod, output=str, error=str).split()
     for i, word in enumerate(text):
         if word == 'conflict':
+<<<<<<< HEAD
             exec(compile(modulecmd('unload', text[
                  i + 1], output=str, error=str), '<string>', 'exec'))
+=======
+            exec(compile(modulecmd('unload', text[i + 1], output=str,
+                                   error=str), '<string>', 'exec'))
+>>>>>>> aa86488fd9809ced16704e4bd4d607c89d6dda75
     # Load the module now that there are no conflicts
     load = modulecmd('load', mod, output=str, error=str)
     exec(compile(load, '<string>', 'exec'))
@@ -239,8 +244,13 @@ def set_build_environment_variables(pkg, env):
     # handled by putting one in the <build_env_path>/case-insensitive
     # directory.  Add that to the path too.
     env_paths = []
+<<<<<<< HEAD
     compiler_specific = join_path(spack.build_env_path, pkg.compiler.name)
     for item in [spack.build_env_path, compiler_specific]:
+=======
+    for item in [spack.build_env_path, join_path(spack.build_env_path,
+                                                 pkg.compiler.name)]:
+>>>>>>> aa86488fd9809ced16704e4bd4d607c89d6dda75
         env_paths.append(item)
         ci = join_path(item, 'case-insensitive')
         if os.path.isdir(ci):
@@ -270,8 +280,13 @@ def set_build_environment_variables(pkg, env):
     env.unset('DYLD_LIBRARY_PATH')
 
     # Add bin directories from dependencies to the PATH for the build.
+<<<<<<< HEAD
     bin_dirs = reversed(
         filter(os.path.isdir, ['%s/bin' % prefix for prefix in dep_prefixes]))
+=======
+    bin_dirs = reversed(filter(os.path.isdir,
+                               ['%s/bin' % prefix for prefix in dep_prefixes]))
+>>>>>>> aa86488fd9809ced16704e4bd4d607c89d6dda75
     for item in bin_dirs:
         env.prepend_path('PATH', item)
 
@@ -286,7 +301,10 @@ def set_build_environment_variables(pkg, env):
         for directory in ('lib', 'lib64', 'share'):
             pcdir = join_path(pre, directory, 'pkgconfig')
             if os.path.isdir(pcdir):
+<<<<<<< HEAD
                 # pkg_config_dirs.append(pcdir)
+=======
+>>>>>>> aa86488fd9809ced16704e4bd4d607c89d6dda75
                 env.prepend_path('PKG_CONFIG_PATH', pcdir)
 
     if pkg.spec.architecture.target.module_name:
@@ -299,7 +317,7 @@ def set_module_variables_for_package(pkg, module):
     """Populate the module scope of install() with some useful functions.
        This makes things easier for package writers.
     """
-    # number of jobs spack will to build with.
+    # number of jobs spack will build with.
     jobs = multiprocessing.cpu_count()
     if not pkg.parallel:
         jobs = 1
@@ -312,6 +330,7 @@ def set_module_variables_for_package(pkg, module):
     # TODO: make these build deps that can be installed if not found.
     m.make = MakeExecutable('make', jobs)
     m.gmake = MakeExecutable('gmake', jobs)
+    m.scons = MakeExecutable('scons', jobs)
 
     # easy shortcut to os.environ
     m.env = os.environ
@@ -325,6 +344,7 @@ def set_module_variables_for_package(pkg, module):
     # TODO: Currently, everything is a link dependency, but tools like
     # TODO: this shouldn't be.
     m.cmake = Executable('cmake')
+    m.ctest = Executable('ctest')
 
     # standard CMake arguments
     m.std_cmake_args = ['-DCMAKE_INSTALL_PREFIX=%s' % pkg.prefix,
@@ -382,9 +402,13 @@ def get_rpaths(pkg):
 
 
 def parent_class_modules(cls):
+<<<<<<< HEAD
     """
     Get list of super class modules that are all descend from spack.Package
     """
+=======
+    """Get list of super class modules that all descend from spack.Package"""
+>>>>>>> aa86488fd9809ced16704e4bd4d607c89d6dda75
     if not issubclass(cls, spack.Package) or issubclass(spack.Package, cls):
         return []
     result = []

lib/spack/spack/cmd/create.py

@@ -1,4 +1,3 @@
-_copyright = """\
 ##############################################################################
 # Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
@@ -23,10 +22,8 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-"""
 import string
 import os
-import hashlib
 import re
 
 from ordereddict_backport import OrderedDict
@@ -41,16 +38,37 @@
 from spack.spec import Spec
 from spack.util.naming import *
 from spack.repository import Repo, RepoError
-import spack.util.crypto as crypto
 
 from spack.util.executable import which
-from spack.stage import Stage
 
 
 description = "Create a new package file from an archive URL"
 
-package_template = string.Template(
+package_template = string.Template("""\
-    _copyright + """
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
 #
 # This is a template package file for Spack.  We've put "FIXME"
 # next to all the things you'll want to change. Once you've handled
@@ -68,24 +86,21 @@
 #
 from spack import *
 
+
 class ${class_name}(Package):
-    ""\"FIXME: put a proper description of your package here.""\"
+    ""\"FIXME: Put a proper description of your package here.""\"
-    # FIXME: add a proper url for your package's homepage here.
+
+    # FIXME: Add a proper url for your package's homepage here.
     homepage = "http://www.example.com"
     url      = "${url}"
 
 ${versions}
-
+${extends}
     # FIXME: Add dependencies if this package requires them.
     # depends_on("foo")
 
     def install(self, spec, prefix):
-        # FIXME: Modify the configure line to suit your build system here.
+${install}
-        ${configure}
-
-        # FIXME: Add logic to build and install here
-        make()
-        make("install")
 """)
 
 
@@ -120,41 +135,95 @@ def setup_parser(subparser):
 
 class ConfigureGuesser(object):
     def __call__(self, stage):
-        """Try to guess the type of build system used by the project, and return
+        """Try to guess the type of build system used by the project.
-           an appropriate configure line.
+        Set the appropriate default installation instructions and any
-        """
+        necessary extensions for Python and R."""
-        autotools = "configure('--prefix=%s' % prefix)"
-        cmake     = "cmake('.', *std_cmake_args)"
-        python    = "python('setup.py', 'install', '--prefix=%s' % prefix)"
-        r         = "R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)"
 
-        config_lines = ((r'/configure$',      'autotools', autotools),
+        # Default installation instructions
-                        (r'/CMakeLists.txt$', 'cmake',     cmake),
+        installDict = {
-                        (r'/setup.py$',       'python',    python),
+            'autotools': """\
-                        (r'/NAMESPACE$',      'r',         r))
+        # FIXME: Modify the configure line to suit your build system here.
+        configure('--prefix={0}'.format(prefix))
 
-        # Peek inside the tarball.
+        # FIXME: Add logic to build and install here.
-        tar = which('tar')
+        make()
-        output = tar(
+        make('install')""",
-            "--exclude=*/*/*", "-tf", stage.archive_file, output=str)
-        lines = output.split("\n")
 
-        # Set the configure line to the one that matched.
+            'cmake':     """\
-        for pattern, bs, cl in config_lines:
+        with working_dir('spack-build', create=True):
-            if any(re.search(pattern, l) for l in lines):
+            # FIXME: Modify the cmake line to suit your build system here.
-                config_line = cl
+            cmake('..', *std_cmake_args)
-                build_system = bs
+
-                break
+            # FIXME: Add logic to build and install here.
+            make()
+            make('install')""",
+
+            'scons':     """\
+        # FIXME: Add logic to build and install here.
+        scons('prefix={0}'.format(prefix))
+        scons('install')""",
+
+            'python':    """\
+        # FIXME: Add logic to build and install here.
+        python('setup.py', 'install', '--prefix={0}'.format(prefix))""",
+
+            'R':         """\
+        # FIXME: Add logic to build and install here.
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)""",
+
+            'unknown':   """\
+        # FIXME: Unknown build system
+        make()
+        make('install')"""
+        }
+
+        # A list of clues that give us an idea of the build system a package
+        # uses. If the regular expression matches a file contained in the
+        # archive, the corresponding build system is assumed.
+        clues = [
+            (r'/configure$',      'autotools'),
+            (r'/CMakeLists.txt$', 'cmake'),
+            (r'/SConstruct$',     'scons'),
+            (r'/setup.py$',       'python'),
+            (r'/NAMESPACE$',      'R')
+        ]
+
+        # Peek inside the compressed file.
+        if stage.archive_file.endswith('.zip'):
+            try:
+                unzip  = which('unzip')
+                output = unzip('-l', stage.archive_file, output=str)
+            except:
+                output = ''
         else:
-            # None matched -- just put both, with cmake commented out
+            try:
-            config_line =  "# FIXME: Spack couldn't guess one, so here are some options:\n"
+                tar    = which('tar')
-            config_line += "        # " + autotools + "\n"
+                output = tar('--exclude=*/*/*', '-tf',
-            config_line += "        # " + cmake
+                             stage.archive_file, output=str)
-            build_system = 'unknown'
+            except:
+                output = ''
+        lines = output.split('\n')
+
+        # Determine the build system based on the files contained
+        # in the archive.
+        build_system = 'unknown'
+        for pattern, bs in clues:
+            if any(re.search(pattern, l) for l in lines):
+                build_system = bs
 
-        self.configure = config_line
         self.build_system = build_system
 
+        # Set the appropriate default installation instructions
+        self.install = installDict[build_system]
+
+        # Set any necessary extensions for Python and R
+        extensions = ''
+        if build_system in ['python', 'R']:
+            extensions = "\n    extends('{0}')\n".format(build_system)
+
+        self.extends = extensions
+
 
 def guess_name_and_version(url, args):
     # Try to deduce name and version of the new package from the URL
@@ -168,7 +237,7 @@ def guess_name_and_version(url, args):
     else:
         try:
             name = spack.url.parse_name(url, version)
-        except spack.url.UndetectableNameError, e:
+        except spack.url.UndetectableNameError:
             # Use a user-supplied name if one is present
             tty.die("Couldn't guess a name for this package. Try running:", "",
                     "spack create --name <name> <url>")
@@ -182,7 +251,8 @@ def guess_name_and_version(url, args):
 def find_repository(spec, args):
     # figure out namespace for spec
     if spec.namespace and args.namespace and spec.namespace != args.namespace:
-        tty.die("Namespaces '%s' and '%s' do not match." % (spec.namespace, args.namespace))
+        tty.die("Namespaces '%s' and '%s' do not match." % (spec.namespace,
+                                                            args.namespace))
 
     if not spec.namespace and args.namespace:
         spec.namespace = args.namespace
@@ -193,8 +263,8 @@ def find_repository(spec, args):
         try:
             repo = Repo(repo_path)
             if spec.namespace and spec.namespace != repo.namespace:
-                tty.die("Can't create package with namespace %s in repo with namespace %s"
+                tty.die("Can't create package with namespace %s in repo with "
-                        % (spec.namespace, repo.namespace))
+                        "namespace %s" % (spec.namespace, repo.namespace))
         except RepoError as e:
             tty.die(str(e))
     else:
@@ -214,11 +284,7 @@ def find_repository(spec, args):
 
 def fetch_tarballs(url, name, version):
     """Try to find versions of the supplied archive by scraping the web.
-
+    Prompts the user to select how many to download if many are found."""
-    Prompts the user to select how many to download if many are found.
-
-
-    """
     versions = spack.util.web.find_versions_of_archive(url)
     rkeys = sorted(versions.keys(), reverse=True)
     versions = OrderedDict(zip(rkeys, (versions[v] for v in rkeys)))
@@ -226,11 +292,11 @@ def fetch_tarballs(url, name, version):
     archives_to_fetch = 1
     if not versions:
         # If the fetch failed for some reason, revert to what the user provided
-        versions = { version : url }
+        versions = {version: url}
     elif len(versions) > 1:
         tty.msg("Found %s versions of %s:" % (len(versions), name),
                 *spack.cmd.elide_list(
-                    ["%-10s%s" % (v,u) for v, u in versions.iteritems()]))
+                    ["%-10s%s" % (v, u) for v, u in versions.iteritems()]))
         print
         archives_to_fetch = tty.get_number(
             "Include how many checksums in the package file?",
@@ -277,7 +343,7 @@ def create(parser, args):
         name = 'py-%s' % name
 
     # Prepend 'r-' to R package names, by convention.
-    if guesser.build_system == 'r':
+    if guesser.build_system == 'R':
         name = 'r-%s' % name
 
     # Create a directory for the new package.
@@ -292,10 +358,11 @@ def create(parser, args):
         pkg_file.write(
             package_template.substitute(
                 name=name,
-                configure=guesser.configure,
                 class_name=mod_to_class(name),
                 url=url,
-                versions=make_version_calls(ver_hash_tuples)))
+                versions=make_version_calls(ver_hash_tuples),
+                extends=guesser.extends,
+                install=guesser.install))
 
     # If everything checks out, go ahead and edit.
     spack.editor(pkg_path)

var/spack/repos/builtin/packages/cantera/package.py

@@ -0,0 +1,197 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+import os
+
+
+class Cantera(Package):
+    """Cantera is a suite of object-oriented software tools for problems
+    involving chemical kinetics, thermodynamics, and/or transport processes."""
+
+    homepage = "http://www.cantera.org/docs/sphinx/html/index.html"
+    url      = "https://github.com/Cantera/cantera/archive/v2.2.1.tar.gz"
+
+    version('2.2.1', '9d1919bdef39ddec54485fc8a741a3aa')
+
+    variant('lapack',     default=True,  description='Build with external BLAS/LAPACK libraries')
+    variant('threadsafe', default=True,  description='Build threadsafe, requires Boost')
+    variant('sundials',   default=True,  description='Build with external Sundials')
+    variant('python',     default=False, description='Build the Cantera Python module')
+    variant('matlab',     default=False, description='Build the Cantera Matlab toolbox')
+
+    # Required dependencies
+    depends_on('scons')
+
+    # Recommended dependencies
+    depends_on('blas',      when='+lapack')
+    depends_on('lapack',    when='+lapack')
+    depends_on('boost',     when='+threadsafe')
+    depends_on('sundials',  when='+sundials')  # must be compiled with -fPIC
+
+    # Python module dependencies
+    extends('python', when='+python')
+    depends_on('py-numpy',  when='+python')
+    depends_on('py-scipy',  when='+python')
+    depends_on('py-cython', when='+python')
+    depends_on('py-3to2',   when='+python')
+    # TODO: these "when" specs don't actually work
+    # depends_on('py-unittest2',     when='+python^python@2.6')
+    # depends_on('py-unittest2py3k', when='+python^python@3.1')
+
+    # Matlab toolbox dependencies
+    # TODO: add Matlab package
+    # TODO: allow packages to extend multiple other packages
+    # extends('matlab',   when='+matlab')
+
+    def install(self, spec, prefix):
+        # Required options
+        options = [
+            'prefix={0}'.format(prefix),
+            'CC={0}'.format(os.environ['CC']),
+            'CXX={0}'.format(os.environ['CXX']),
+            'F77={0}'.format(os.environ['F77']),
+            'FORTRAN={0}'.format(os.environ['FC']),
+            'cc_flags=-fPIC',
+            # Allow Spack environment variables to propagate through to SCons
+            'env_vars=all'
+        ]
+
+        # BLAS/LAPACK support
+        if '+lapack' in spec:
+            options.extend([
+                'blas_lapack_libs=lapack,blas',
+                'blas_lapack_dir={0}'.format(spec['lapack'].prefix.lib)
+            ])
+
+        # Threadsafe build, requires Boost
+        if '+threadsafe' in spec:
+            options.extend([
+                'build_thread_safe=yes',
+                'boost_inc_dir={0}'.format(spec['boost'].prefix.include),
+                'boost_lib_dir={0}'.format(spec['boost'].prefix.lib),
+                'boost_thread_lib=boost_thread-mt,boost_system-mt'
+            ])
+        else:
+            options.append('build_thread_safe=no')
+
+        # Sundials support
+        if '+sundials' in spec:
+            options.extend([
+                'use_sundials=y',
+                'sundials_include={0}'.format(spec['sundials'].prefix.include),
+                'sundials_libdir={0}'.format(spec['sundials'].prefix.lib),
+                'sundials_license={0}'.format(
+                    join_path(spec['sundials'].prefix, 'LICENSE'))
+            ])
+        else:
+            options.append('use_sundials=n')
+
+        # Python module
+        if '+python' in spec:
+            options.extend([
+                'python_package=full',
+                'python_cmd={0}'.format(
+                    join_path(spec['python'].prefix.bin, 'python')),
+                'python_array_home={0}'.format(spec['py-numpy'].prefix)
+            ])
+            if spec['python'].satisfies('@3'):
+                options.extend([
+                    'python3_package=y',
+                    'python3_cmd={0}'.format(
+                        join_path(spec['python'].prefix.bin, 'python')),
+                    'python3_array_home={0}'.format(spec['py-numpy'].prefix)
+                ])
+            else:
+                options.append('python3_package=n')
+        else:
+            options.append('python_package=none')
+            options.append('python3_package=n')
+
+        # Matlab toolbox
+        if '+matlab' in spec:
+            options.extend([
+                'matlab_toolbox=y',
+                'matlab_path={0}'.format(spec['matlab'].prefix)
+            ])
+        else:
+            options.append('matlab_toolbox=n')
+
+        scons('build', *options)
+
+        if '+python' in spec:
+            # Tests will always fail if Python dependencies aren't built
+            # In addition, 3 of the tests fail when run in parallel
+            scons('test', parallel=False)
+
+        scons('install')
+
+        self.filter_compilers()
+
+    def filter_compilers(self):
+        """Run after install to tell the Makefile and SConstruct files to use
+        the compilers that Spack built the package with.
+
+        If this isn't done, they'll have CC, CXX, F77, and FC set to Spack's
+        generic cc, c++, f77, and f90. We want them to be bound to whatever
+        compiler they were built with."""
+
+        kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
+        dirname = os.path.join(self.prefix, 'share/cantera/samples')
+
+        cc_files = [
+            'cxx/rankine/Makefile',   'cxx/NASA_coeffs/Makefile',
+            'cxx/kinetics1/Makefile', 'cxx/flamespeed/Makefile',
+            'cxx/combustor/Makefile', 'f77/SConstruct'
+        ]
+
+        cxx_files = [
+            'cxx/rankine/Makefile',   'cxx/NASA_coeffs/Makefile',
+            'cxx/kinetics1/Makefile', 'cxx/flamespeed/Makefile',
+            'cxx/combustor/Makefile'
+        ]
+
+        f77_files = [
+            'f77/Makefile', 'f77/SConstruct'
+        ]
+
+        fc_files = [
+            'f90/Makefile', 'f90/SConstruct'
+        ]
+
+        for filename in cc_files:
+            filter_file(os.environ['CC'], self.compiler.cc,
+                        os.path.join(dirname, filename), **kwargs)
+
+        for filename in cxx_files:
+            filter_file(os.environ['CXX'], self.compiler.cxx,
+                        os.path.join(dirname, filename), **kwargs)
+
+        for filename in f77_files:
+            filter_file(os.environ['F77'], self.compiler.f77,
+                        os.path.join(dirname, filename), **kwargs)
+
+        for filename in fc_files:
+            filter_file(os.environ['FC'], self.compiler.fc,
+                        os.path.join(dirname, filename), **kwargs)

var/spack/repos/builtin/packages/py-3to2/package.py

@@ -0,0 +1,40 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Py3to2(Package):
+    """lib3to2 is a set of fixers that are intended to backport code written
+    for Python version 3.x into Python version 2.x."""
+
+    homepage = "https://pypi.python.org/pypi/3to2"
+    url      = "https://pypi.python.org/packages/source/3/3to2/3to2-1.1.1.zip"
+
+    version('1.1.1', 'cbeed28e350dbdaef86111ace3052824')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/repos/builtin/packages/py-unittest2/package.py

@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class PyUnittest2(Package):
+    """unittest2 is a backport of the new features added to the unittest
+    testing framework in Python 2.7 and onwards."""
+
+    homepage = "https://pypi.python.org/pypi/unittest2"
+    url      = "https://pypi.python.org/packages/source/u/unittest2/unittest2-1.1.0.tar.gz"
+
+    version('1.1.0', 'f72dae5d44f091df36b6b513305ea000')
+
+    extends('python')
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/repos/builtin/packages/py-unittest2py3k/package.py

@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class PyUnittest2py3k(Package):
+    """unittest2 is a backport of the new features added to the unittest
+    testing framework in Python 2.7 and 3.2. This is a Python 3 compatible
+    version of unittest2."""
+
+    homepage = "https://pypi.python.org/pypi/unittest2py3k"
+    url      = "https://pypi.python.org/packages/source/u/unittest2py3k/unittest2py3k-0.5.1.tar.gz"
+
+    version('0.5.1', '8824ff92044310d9365f90d892bf0f09')
+
+    extends('python')
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/repos/builtin/packages/serf/package.py

@@ -28,10 +28,11 @@
 class Serf(Package):
     """Apache Serf - a high performance C-based HTTP client library
     built upon the Apache Portable Runtime (APR) library"""
+
     homepage  = 'https://serf.apache.org/'
     url       = 'https://archive.apache.org/dist/serf/serf-1.3.8.tar.bz2'
 
-    version('1.3.8',     '1d45425ca324336ce2f4ae7d7b4cfbc5567c5446')
+    version('1.3.8', '1d45425ca324336ce2f4ae7d7b4cfbc5567c5446')
 
     depends_on('apr')
     depends_on('apr-util')
@@ -41,8 +42,6 @@ class Serf(Package):
     depends_on('zlib')
 
     def install(self, spec, prefix):
-        scons = which("scons")
-
         options = ['PREFIX=%s' % prefix]
         options.append('APR=%s' % spec['apr'].prefix)
         options.append('APU=%s' % spec['apr-util'].prefix)

var/spack/repos/builtin/packages/sundials/package.py

@@ -23,17 +23,151 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+import os
+
 
 class Sundials(Package):
-    """SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation Solvers)"""
+    """SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation
+    Solvers)"""
+
     homepage = "http://computation.llnl.gov/casc/sundials/"
-    url      = "http://computation.llnl.gov/casc/sundials/download/code/sundials-2.5.0.tar.gz"
+    url      = "http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers/download/sundials-2.6.2.tar.gz"
 
-    version('2.5.0', 'aba8b56eec600de3109cfb967aa3ba0f')
+    version('2.6.2', '3deeb0ede9f514184c6bd83ecab77d95')
 
-    depends_on("mpi")
+    variant('mpi',     default=True,  description='Enable MPI support')
+    variant('lapack',  default=True,  description='Build with external BLAS/LAPACK libraries')
+    variant('klu',     default=False, description='Build with SuiteSparse KLU libraries')
+    variant('superlu', default=False, description='Build with SuperLU_MT libraries')
+    variant('openmp',  default=False, description='Enable OpenMP support')
+    variant('pthread', default=True,  description='Enable POSIX threads support')
+
+    depends_on('mpi',                when='+mpi')
+    depends_on('blas',               when='+lapack')
+    depends_on('lapack',             when='+lapack')
+    depends_on('suite-sparse',       when='+klu')
+    depends_on('superlu-mt+openmp',  when='+superlu+openmp')
+    depends_on('superlu-mt+pthread', when='+superlu+pthread')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix)
+        cmake_args = std_cmake_args[:]
-        make()
+        cmake_args.extend([
-        make("install")
+            '-DBUILD_SHARED_LIBS=ON',
+            '-DCMAKE_C_FLAGS=-fPIC',
+            '-DCMAKE_Fortran_FLAGS=-fPIC',
+            '-DEXAMPLES_ENABLE=ON',
+            '-DEXAMPLES_INSTALL=ON',
+            '-DFCMIX_ENABLE=ON'
+        ])
+
+        # MPI support
+        if '+mpi' in spec:
+            cmake_args.extend([
+                '-DMPI_ENABLE=ON',
+                '-DMPI_MPICC={0}'.format(spec['mpi'].mpicc),
+                '-DMPI_MPIF77={0}'.format(spec['mpi'].mpif77)
+            ])
+        else:
+            cmake_args.append('-DMPI_ENABLE=OFF')
+
+        # Building with LAPACK and BLAS
+        if '+lapack' in spec:
+            cmake_args.extend([
+                '-DLAPACK_ENABLE=ON',
+                '-DLAPACK_LIBRARIES={0};{1}'.format(
+                    spec['lapack'].lapack_shared_lib,
+                    spec['blas'].blas_shared_lib
+                )
+            ])
+        else:
+            cmake_args.append('-DLAPACK_ENABLE=OFF')
+
+        # Building with KLU
+        if '+klu' in spec:
+            cmake_args.extend([
+                '-DKLU_ENABLE=ON',
+                '-DKLU_INCLUDE_DIR={0}'.format(
+                    spec['suite-sparse'].prefix.include),
+                '-DKLU_LIBRARY_DIR={0}'.format(
+                    spec['suite-sparse'].prefix.lib)
+            ])
+        else:
+            cmake_args.append('-DKLU_ENABLE=OFF')
+
+        # Building with SuperLU_MT
+        if '+superlu' in spec:
+            cmake_args.extend([
+                '-DSUPERLUMT_ENABLE=ON',
+                '-DSUPERLUMT_INCLUDE_DIR={0}'.format(
+                    spec['superlu-mt'].prefix.include),
+                '-DSUPERLUMT_LIBRARY_DIR={0}'.format(
+                    spec['superlu-mt'].prefix.lib)
+            ])
+            if '+openmp' in spec:
+                cmake_args.append('-DSUPERLUMT_THREAD_TYPE=OpenMP')
+            elif '+pthread' in spec:
+                cmake_args.append('-DSUPERLUMT_THREAD_TYPE=Pthread')
+            else:
+                msg  = 'You must choose either +openmp or +pthread when '
+                msg += 'building with SuperLU_MT'
+                raise RuntimeError(msg)
+        else:
+            cmake_args.append('-DSUPERLUMT_ENABLE=OFF')
+
+        # OpenMP support
+        if '+openmp' in spec:
+            cmake_args.append('-DOPENMP_ENABLE=ON')
+        else:
+            cmake_args.append('-DOPENMP_ENABLE=OFF')
+
+        # POSIX threads support
+        if '+pthread' in spec:
+            cmake_args.append('-DPTHREAD_ENABLE=ON')
+        else:
+            cmake_args.append('-DPTHREAD_ENABLE=OFF')
+
+        with working_dir('build', create=True):
+            cmake('..', *cmake_args)
+
+            make()
+            make('install')
+
+        install('LICENSE', prefix)
+
+        self.filter_compilers()
+
+    def filter_compilers(self):
+        """Run after install to tell the Makefiles to use
+        the compilers that Spack built the package with.
+
+        If this isn't done, they'll have CC, CPP, and F77 set to
+        Spack's generic cc and f77. We want them to be bound to
+        whatever compiler they were built with."""
+
+        kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
+        dirname = os.path.join(self.prefix, 'examples')
+
+        cc_files = [
+            'arkode/C_serial/Makefile',  'arkode/C_parallel/Makefile',
+            'cvode/serial/Makefile',     'cvode/parallel/Makefile',
+            'cvodes/serial/Makefile',    'cvodes/parallel/Makefile',
+            'ida/serial/Makefile',       'ida/parallel/Makefile',
+            'idas/serial/Makefile',      'idas/parallel/Makefile',
+            'kinsol/serial/Makefile',    'kinsol/parallel/Makefile',
+            'nvector/serial/Makefile',   'nvector/parallel/Makefile',
+            'nvector/pthreads/Makefile'
+        ]
+
+        f77_files = [
+            'arkode/F77_serial/Makefile', 'cvode/fcmix_serial/Makefile',
+            'ida/fcmix_serial/Makefile',  'ida/fcmix_pthreads/Makefile',
+            'kinsol/fcmix_serial/Makefile'
+        ]
+
+        for filename in cc_files:
+            filter_file(os.environ['CC'], self.compiler.cc,
+                        os.path.join(dirname, filename), **kwargs)
+
+        for filename in f77_files:
+            filter_file(os.environ['F77'], self.compiler.f77,
+                        os.path.join(dirname, filename), **kwargs)

var/spack/repos/builtin/packages/superlu-mt/package.py

@@ -0,0 +1,134 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+import glob
+import os
+
+
+class SuperluMt(Package):
+    """SuperLU is a general purpose library for the direct solution of large,
+    sparse, nonsymmetric systems of linear equations on high performance
+    machines. SuperLU_MT is designed for shared memory parallel machines."""
+
+    homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/#superlu_mt"
+    url      = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_mt_3.1.tar.gz"
+
+    version('3.1', '06ac62f1b4b7d17123fffa0d0c315e91')
+
+    variant('blas',    default=True,  description='Build with external BLAS library')
+
+    # Must choose one or the other
+    variant('openmp',  default=False, description='Build with OpenMP support')
+    variant('pthread', default=True,  description='Build with POSIX threads support')
+
+    # NOTE: must link with a single-threaded BLAS library
+    depends_on('blas', when='+blas')
+
+    # Cannot be built in parallel
+    parallel = False
+
+    def configure(self, spec):
+        # Validate chosen variants
+        if '+openmp' in spec and '+pthread' in spec:
+            msg = 'You cannot choose both +openmp and +pthread'
+            raise RuntimeError(msg)
+        if '~openmp' in spec and '~pthread' in spec:
+            msg = 'You must choose either +openmp or +pthread'
+            raise RuntimeError(msg)
+
+        # List of configuration options
+        config = []
+
+        # The machine (platform) identifier to append to the library names
+        if '+openmp' in spec:
+            # OpenMP
+            config.extend([
+                'PLAT       = _OPENMP',
+                'TMGLIB     = libtmglib.a',
+                'MPLIB      = {0}'.format(self.compiler.openmp_flag),
+                'CFLAGS     = {0}'.format(self.compiler.openmp_flag),
+                'FFLAGS     = {0}'.format(self.compiler.openmp_flag)
+            ])
+        elif '+pthread' in spec:
+            # POSIX threads
+            config.extend([
+                'PLAT       = _PTHREAD',
+                'TMGLIB     = libtmglib$(PLAT).a',
+                'MPLIB      = -lpthread'
+            ])
+
+        # The BLAS library
+        # NOTE: must link with a single-threaded BLAS library
+        if '+blas' in spec:
+            config.extend([
+                'BLASDEF    = -DUSE_VENDOR_BLAS',
+                'BLASLIB    = -L{0} -lblas'.format(spec['blas'].prefix.lib)
+            ])
+        else:
+            config.append('BLASLIB    = ../lib/libblas$(PLAT).a')
+
+        # Generic options
+        config.extend([
+            # The name of the libraries to be created/linked to
+            'SUPERLULIB = libsuperlu_mt$(PLAT).a',
+            'MATHLIB    = -lm',
+            # The archiver and the flag(s) to use when building archives
+            'ARCH       = ar',
+            'ARCHFLAGS  = cr',
+            'RANLIB     = {0}'.format('ranlib' if which('ranlib') else 'echo'),
+            # Definitions used by CPP
+            'PREDEFS    = -D_$(PLAT)',
+            # Compilers and flags
+            'CC         = {0}'.format(os.environ['CC']),
+            'CFLAGS    += $(PREDEFS) -D_LONGINT',
+            'NOOPTS     = -O0',
+            'FORTRAN    = {0}'.format(os.environ['FC']),
+            'LOADER     = {0}'.format(os.environ['CC']),
+            # C preprocessor defs for compilation
+            'CDEFS      = -DAdd_'
+        ])
+
+        # Write configuration options to include file
+        with open('make.inc', 'w') as inc:
+            for option in config:
+                inc.write('{0}\n'.format(option))
+
+    def install(self, spec, prefix):
+        # Set up make include file manually
+        self.configure(spec)
+
+        # BLAS needs to be compiled separately if using internal BLAS library
+        if '+blas' not in spec:
+            make('blaslib')
+
+        make()
+
+        # Install manually
+        install_tree('lib', prefix.lib)
+
+        headers = glob.glob(join_path('SRC', '*.h'))
+        mkdir(prefix.include)
+        for h in headers:
+            install(h, prefix.include)