Merge branch 'develop' of https://github.com/LLNL/spack into features/module_refresh

Conflicts:
	share/spack/setup-env.sh

lib/spack/docs/basic_usage.rst

@@ -183,7 +183,7 @@ To uninstall a package and every package that depends on it, you may give the
 
    spack uninstall --dependents mpich
 
-will display a list of all the packages that depends on `mpich` and, upon confirmation,
+will display a list of all the packages that depend on `mpich` and, upon confirmation,
 will uninstall them in the right order.
 
 A line like
@@ -543,11 +543,12 @@ More formally, a spec consists of the following pieces:
 * ``+`` or ``-`` or ``~`` Optional variant specifiers (``+debug``,
   ``-qt``, or ``~qt``) for boolean variants
 * ``name=<value>`` Optional variant specifiers that are not restricted to
-boolean variants
+  boolean variants
 * ``name=<value>`` Optional compiler flag specifiers. Valid flag names are
-``cflags``, ``cxxflags``, ``fflags``, ``cppflags``, ``ldflags``, and ``ldlibs``.
+  ``cflags``, ``cxxflags``, ``fflags``, ``cppflags``, ``ldflags``, and ``ldlibs``.
 * ``target=<value> os=<value>`` Optional architecture specifier 
-(``target=haswell os=CNL10``) * ``^`` Dependency specs (``^callpath@1.1``)
+  (``target=haswell os=CNL10``)
+* ``^`` Dependency specs (``^callpath@1.1``)
 
 There are two things to notice here.  The first is that specs are
 recursively defined.  That is, each dependency after ``^`` is a spec

lib/spack/docs/packaging_guide.rst

@@ -2627,14 +2627,14 @@ Spack packages with variants similar to already-existing Spack
 packages should use the same name for their variants.  Standard
 variant names are:
 
-======= ======== ========================
+  ======= ======== ========================
-Name    Default   Description
+  Name    Default   Description
-------- -------- ------------------------
+  ======= ======== ========================
-shared   True     Build shared libraries
+  shared   True     Build shared libraries
-static            Build static libraries
+  static            Build static libraries
-mpi               Use MPI
+  mpi               Use MPI
-python            Build Python extension
+  python            Build Python extension
-------- -------- ------------------------
+  ======= ======== ========================
 
 If specified in this table, the corresponding default should be used
 when declaring a variant.

lib/spack/llnl/util/filesystem.py

@@ -42,7 +42,7 @@
            'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink',
            'set_executable', 'copy_mode', 'unset_executable_mode',
            'remove_dead_links', 'remove_linked_tree', 'find_library_path',
-           'fix_darwin_install_name', 'to_link_flags']
+           'fix_darwin_install_name', 'to_link_flags', 'to_lib_name']
 
 
 def filter_file(regex, repl, *filenames, **kwargs):
@@ -431,6 +431,13 @@ def fix_darwin_install_name(path):
                     break
 
 
+def to_lib_name(library):
+    """Transforms a path to the library /path/to/lib<name>.xyz into <name>
+    """
+    # Assume libXYZ.suffix
+    return os.path.basename(library)[3:].split(".")[0]
+
+
 def to_link_flags(library):
     """Transforms a path to a <library> into linking flags -L<dir> -l<name>.
 
@@ -438,8 +445,7 @@ def to_link_flags(library):
       A string of linking flags.
     """
     dir  = os.path.dirname(library)
-    # Assume libXYZ.suffix
+    name = to_lib_name(library)
-    name = os.path.basename(library)[3:].split(".")[0]
     res = '-L%s -l%s' % (dir, name)
     return res
 

lib/spack/spack/cmd/create.py

@@ -142,9 +142,9 @@ def __call__(self, stage):
         # Build dependencies and extensions
         dependenciesDict = {
             'autotools': "# depends_on('foo')",
-            'cmake':     "depends_on('cmake')",
+            'cmake':     "depends_on('cmake', type='build')",
-            'scons':     "depends_on('scons')",
+            'scons':     "depends_on('scons', type='build')",
-            'python':    "extends('python')",
+            'python':    "extends('python', type=nolink)",
             'R':         "extends('R')",
             'unknown':   "# depends_on('foo')"
         }

lib/spack/spack/cmd/info.py

@@ -29,9 +29,11 @@
 
 description = "Get detailed information on a particular package"
 
+
 def padder(str_list, extra=0):
     """Return a function to pad elements of a list."""
     length = max(len(str(s)) for s in str_list) + extra
+
     def pad(string):
         string = str(string)
         padding = max(0, length - len(string))
@@ -40,7 +42,8 @@ def pad(string):
 
 
 def setup_parser(subparser):
-    subparser.add_argument('name', metavar="PACKAGE", help="Name of package to get info for.")
+    subparser.add_argument(
+        'name', metavar="PACKAGE", help="Name of package to get info for.")
 
 
 def print_text_info(pkg):
@@ -84,7 +87,7 @@ def print_text_info(pkg):
     for deptype in ('build', 'link', 'run'):
         print
         print "%s Dependencies:" % deptype.capitalize()
-        deps = pkg.dependencies(deptype)
+        deps = pkg.dependencies_of_type(deptype)
         if deps:
             colify(deps, indent=4)
         else:

lib/spack/spack/database.py

@@ -60,7 +60,7 @@
 _db_dirname = '.spack-db'
 
 # DB version.  This is stuck in the DB file to track changes in format.
-_db_version = Version('0.9.1')
+_db_version = Version('0.9.2')
 
 # Default timeout for spack database locks is 5 min.
 _db_lock_timeout = 60
@@ -215,14 +215,10 @@ def _read_spec_from_yaml(self, hash_key, installs, parent_key=None):
         # Add dependencies from other records in the install DB to
         # form a full spec.
         if 'dependencies' in spec_dict[spec.name]:
-            for dep in spec_dict[spec.name]['dependencies'].values():
+            yaml_deps = spec_dict[spec.name]['dependencies']
-                if type(dep) == tuple:
+            for dname, dhash, dtypes in Spec.read_yaml_dep_specs(yaml_deps):
-                    dep_hash, deptypes = dep
+                child = self._read_spec_from_yaml(dhash, installs, hash_key)
-                else:
+                spec._add_dependency(child, dtypes)
-                    dep_hash = dep
-                    deptypes = spack.alldeps
-                child = self._read_spec_from_yaml(dep_hash, installs, hash_key)
-                spec._add_dependency(child, deptypes)
 
         # Specs from the database need to be marked concrete because
         # they represent actual installations.
@@ -639,13 +635,14 @@ def _exit(self):
 class CorruptDatabaseError(SpackError):
     def __init__(self, path, msg=''):
         super(CorruptDatabaseError, self).__init__(
-            "Spack database is corrupt: %s.  %s." + \
+            "Spack database is corrupt: %s.  %s." % (path, msg),
-            "Try running `spack reindex` to fix." % (path, msg))
+            "Try running `spack reindex` to fix.")
 
 
 class InvalidDatabaseVersionError(SpackError):
     def __init__(self, expected, found):
         super(InvalidDatabaseVersionError, self).__init__(
-            "Expected database version %s but found version %s." + \
+            "Expected database version %s but found version %s."
-            "Try running `spack reindex` to fix." %
+            % (expected, found),
-            (expected, found))
+            "`spack reindex` may fix this, or you may need a newer "
+            "Spack version.")

lib/spack/spack/directory_layout.py

@@ -34,6 +34,7 @@
 import llnl.util.tty as tty
 from llnl.util.filesystem import join_path, mkdirp
 
+import spack
 from spack.spec import Spec
 from spack.error import SpackError
 
@@ -223,8 +224,14 @@ def write_spec(self, spec, path):
 
     def read_spec(self, path):
         """Read the contents of a file and parse them as a spec"""
+        try:
             with open(path) as f:
                 spec = Spec.from_yaml(f)
+        except Exception as e:
+            if spack.debug:
+                raise
+            raise SpecReadError(
+                'Unable to read file: %s' % path, 'Cause: ' + str(e))
 
         # Specs read from actual installations are always concrete
         spec._mark_concrete()
@@ -456,10 +463,12 @@ def __init__(self, path):
             "Install path %s already exists!")
 
 
+class SpecReadError(DirectoryLayoutError):
+    """Raised when directory layout can't read a spec."""
+
+
 class InvalidExtensionSpecError(DirectoryLayoutError):
     """Raised when an extension file has a bad spec in it."""
-    def __init__(self, message):
-        super(InvalidExtensionSpecError, self).__init__(message)
 
 
 class ExtensionAlreadyInstalledError(DirectoryLayoutError):

lib/spack/spack/package.py

@@ -37,7 +37,6 @@
 import re
 import textwrap
 import time
-import glob
 import string
 
 import llnl.util.tty as tty
@@ -62,10 +61,10 @@
 from spack.stage import Stage, ResourceStage, StageComposite
 from spack.util.compression import allowed_archive
 from spack.util.environment import dump_environment
-from spack.util.executable import ProcessError, Executable, which
+from spack.util.executable import ProcessError, which
 from spack.version import *
 from spack import directory_layout
-from urlparse import urlparse
+
 
 """Allowed URL schemes for spack packages."""
 _ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"]
@@ -410,7 +409,6 @@ def package_dir(self):
         """Return the directory where the package.py file lives."""
         return os.path.dirname(self.module.__file__)
 
-
     @property
     def global_license_dir(self):
         """Returns the directory where global license files for all
@@ -565,6 +563,11 @@ def fetcher(self):
     def fetcher(self, f):
         self._fetcher = f
 
+    def dependencies_of_type(self, *deptypes):
+        """Get subset of the dependencies with certain types."""
+        return dict((name, conds) for name, conds in self.dependencies.items()
+                    if any(d in self._deptypes[name] for d in deptypes))
+
     @property
     def extendee_spec(self):
         """
@@ -687,7 +690,7 @@ def installed_dependents(self):
             if self.name == spec.name:
                 continue
             # XXX(deptype): Should build dependencies not count here?
-            #for dep in spec.traverse(deptype=('run')):
+            # for dep in spec.traverse(deptype=('run')):
             for dep in spec.traverse(deptype=spack.alldeps):
                 if self.spec == dep:
                     dependents.append(spec)
@@ -699,7 +702,7 @@ def prefix(self):
         return self.spec.prefix
 
     @property
-    #TODO: Change this to architecture
+    # TODO: Change this to architecture
     def compiler(self):
         """Get the spack.compiler.Compiler object used to build this package"""
         if not self.spec.concrete:
@@ -761,7 +764,6 @@ def do_fetch(self, mirror_only=False):
 
         self.stage.cache_local()
 
-
     def do_stage(self, mirror_only=False):
         """Unpacks the fetched tarball, then changes into the expanded tarball
            directory."""
@@ -879,6 +881,7 @@ def _resource_stage(self, resource):
         return resource_stage_folder
 
     install_phases = set(['configure', 'build', 'install', 'provenance'])
+
     def do_install(self,
                    keep_prefix=False,
                    keep_stage=False,
@@ -890,7 +893,7 @@ def do_install(self,
                    fake=False,
                    explicit=False,
                    dirty=False,
-                   install_phases = install_phases):
+                   install_phases=install_phases):
         """Called by commands to install a package and its dependencies.
 
         Package implementations should override install() to describe
@@ -911,7 +914,8 @@ def do_install(self,
         run_tests   -- Runn tests within the package's install()
         """
         if not self.spec.concrete:
-            raise ValueError("Can only install concrete packages: %s." % self.spec.name)
+            raise ValueError("Can only install concrete packages: %s."
+                             % self.spec.name)
 
         # No installation needed if package is external
         if self.spec.external:
@@ -920,7 +924,8 @@ def do_install(self,
             return
 
         # Ensure package is not already installed
-        if 'install' in install_phases and spack.install_layout.check_installed(self.spec):
+        layout = spack.install_layout
+        if 'install' in install_phases and layout.check_installed(self.spec):
             tty.msg("%s is already installed in %s" % (self.name, self.prefix))
             rec = spack.installed_db.get_record(self.spec)
             if (not rec.explicit) and explicit:
@@ -1001,20 +1006,17 @@ def build_process():
                     if 'install' in self.install_phases:
                         self.sanity_check_prefix()
 
-
                     # Copy provenance into the install directory on success
                     if 'provenance' in self.install_phases:
-                        log_install_path = spack.install_layout.build_log_path(
+                        log_install_path = layout.build_log_path(self.spec)
-                            self.spec)
+                        env_install_path = layout.build_env_path(self.spec)
-                        env_install_path = spack.install_layout.build_env_path(
+                        packages_dir = layout.build_packages_path(self.spec)
-                            self.spec)
-                        packages_dir = spack.install_layout.build_packages_path(
-                            self.spec)
 
                         # Remove first if we're overwriting another build
                         # (can happen with spack setup)
                         try:
-                            shutil.rmtree(packages_dir)   # log_install_path and env_install_path are inside this
+                            # log_install_path and env_install_path are here
+                            shutil.rmtree(packages_dir)
                         except:
                             pass
 
@@ -1041,7 +1043,7 @@ def build_process():
         except directory_layout.InstallDirectoryAlreadyExistsError:
             if 'install' in install_phases:
                 # Abort install if install directory exists.
-                # But do NOT remove it (you'd be overwriting someon else's stuff)
+                # But do NOT remove it (you'd be overwriting someone's data)
                 tty.warn("Keeping existing install prefix in place.")
                 raise
             else:
@@ -1533,24 +1535,29 @@ def _hms(seconds):
         parts.append("%.2fs" % s)
     return ' '.join(parts)
 
+
 class StagedPackage(Package):
     """A Package subclass where the install() is split up into stages."""
 
     def install_setup(self):
-        """Creates an spack_setup.py script to configure the package later if we like."""
+        """Creates a spack_setup.py script to configure the package later."""
-        raise InstallError("Package %s provides no install_setup() method!" % self.name)
+        raise InstallError(
+            "Package %s provides no install_setup() method!" % self.name)
 
     def install_configure(self):
         """Runs the configure process."""
-        raise InstallError("Package %s provides no install_configure() method!" % self.name)
+        raise InstallError(
+            "Package %s provides no install_configure() method!" % self.name)
 
     def install_build(self):
         """Runs the build process."""
-        raise InstallError("Package %s provides no install_build() method!" % self.name)
+        raise InstallError(
+            "Package %s provides no install_build() method!" % self.name)
 
     def install_install(self):
         """Runs the install process."""
-        raise InstallError("Package %s provides no install_install() method!" % self.name)
+        raise InstallError(
+            "Package %s provides no install_install() method!" % self.name)
 
     def install(self, spec, prefix):
         if 'setup' in self.install_phases:
@@ -1567,9 +1574,10 @@ def install(self, spec, prefix):
         else:
             # Create a dummy file so the build doesn't fail.
             # That way, the module file will also be created.
-            with open(os.path.join(prefix, 'dummy'), 'w') as fout:
+            with open(os.path.join(prefix, 'dummy'), 'w'):
                 pass
 
+
 # stackoverflow.com/questions/12791997/how-do-you-do-a-simple-chmod-x-from-within-python
 def make_executable(path):
     mode = os.stat(path).st_mode
@@ -1577,9 +1585,7 @@ def make_executable(path):
     os.chmod(path, mode)
 
 
-
 class CMakePackage(StagedPackage):
-
     def make_make(self):
         import multiprocessing
         # number of jobs spack will to build with.
@@ -1593,37 +1599,41 @@ def make_make(self):
         return make
 
     def configure_args(self):
-        """Returns package-specific arguments to be provided to the configure command."""
+        """Returns package-specific arguments to be provided to
+           the configure command.
+        """
         return list()
 
     def configure_env(self):
-        """Returns package-specific environment under which the configure command should be run."""
+        """Returns package-specific environment under which the
+           configure command should be run.
+        """
         return dict()
 
-    def spack_transitive_include_path(self):
+    def transitive_inc_path(self):
         return ';'.join(
             os.path.join(dep, 'include')
             for dep in os.environ['SPACK_DEPENDENCIES'].split(os.pathsep)
         )
 
     def install_setup(self):
-        cmd = [str(which('cmake'))] + \
+        cmd = [str(which('cmake'))]
-            spack.build_environment.get_std_cmake_args(self) + \
+        cmd += spack.build_environment.get_std_cmake_args(self)
-            ['-DCMAKE_INSTALL_PREFIX=%s' % os.environ['SPACK_PREFIX'],
+        cmd += ['-DCMAKE_INSTALL_PREFIX=%s' % os.environ['SPACK_PREFIX'],
                 '-DCMAKE_C_COMPILER=%s' % os.environ['SPACK_CC'],
                 '-DCMAKE_CXX_COMPILER=%s' % os.environ['SPACK_CXX'],
-            '-DCMAKE_Fortran_COMPILER=%s' % os.environ['SPACK_FC']] + \
+                '-DCMAKE_Fortran_COMPILER=%s' % os.environ['SPACK_FC']]
-            self.configure_args()
+        cmd += self.configure_args()
 
-        env = dict()
+        env = {
-        env['PATH'] = os.environ['PATH']
+            'PATH': os.environ['PATH'],
-        env['SPACK_TRANSITIVE_INCLUDE_PATH'] = self.spack_transitive_include_path()
+            'SPACK_TRANSITIVE_INCLUDE_PATH': self.transitive_inc_path(),
-        env['CMAKE_PREFIX_PATH'] = os.environ['CMAKE_PREFIX_PATH']
+            'CMAKE_PREFIX_PATH': os.environ['CMAKE_PREFIX_PATH']
+        }
 
         setup_fname = 'spconfig.py'
         with open(setup_fname, 'w') as fout:
-            fout.write(\
+            fout.write(r"""#!%s
-r"""#!%s
 #
 
 import sys
@@ -1639,34 +1649,39 @@ def cmdlist(str):
             for name in env_vars:
                 val = env[name]
                 if string.find(name, 'PATH') < 0:
-                    fout.write('env[%s] = %s\n' % (repr(name),repr(val)))
+                    fout.write('env[%s] = %s\n' % (repr(name), repr(val)))
                 else:
                     if name == 'SPACK_TRANSITIVE_INCLUDE_PATH':
                         sep = ';'
                     else:
                         sep = ':'
 
-                    fout.write('env[%s] = "%s".join(cmdlist("""\n' % (repr(name),sep))
+                    fout.write('env[%s] = "%s".join(cmdlist("""\n'
+                               % (repr(name), sep))
                     for part in string.split(val, sep):
                         fout.write('    %s\n' % part)
                     fout.write('"""))\n')
 
-            fout.write("env['CMAKE_TRANSITIVE_INCLUDE_PATH'] = env['SPACK_TRANSITIVE_INCLUDE_PATH']   # Deprecated\n")
+            fout.write("env['CMAKE_TRANSITIVE_INCLUDE_PATH'] = "
+                       "env['SPACK_TRANSITIVE_INCLUDE_PATH']   # Deprecated\n")
             fout.write('\ncmd = cmdlist("""\n')
             fout.write('%s\n' % cmd[0])
             for arg in cmd[1:]:
                 fout.write('    %s\n' % arg)
             fout.write('""") + sys.argv[1:]\n')
-            fout.write('\nproc = subprocess.Popen(cmd, env=env)\nproc.wait()\n')
+            fout.write('\nproc = subprocess.Popen(cmd, env=env)\n')
+            fout.write('proc.wait()\n')
         make_executable(setup_fname)
 
-
     def install_configure(self):
         cmake = which('cmake')
         with working_dir(self.build_directory, create=True):
-            os.environ.update(self.configure_env())
+            env = os.environ
-            os.environ['SPACK_TRANSITIVE_INCLUDE_PATH'] = self.spack_transitive_include_path()
+            env.update(self.configure_env())
-            options = self.configure_args() + spack.build_environment.get_std_cmake_args(self)
+            env['SPACK_TRANSITIVE_INCLUDE_PATH'] = self.transitive_inc_path()
+
+            options = self.configure_args()
+            options += spack.build_environment.get_std_cmake_args(self)
             cmake(self.source_directory, *options)
 
     def install_build(self):

lib/spack/spack/spec.py

@@ -96,7 +96,6 @@
 expansion when it is the first character in an id typed on the command line.
 """
 import sys
-import itertools
 import hashlib
 import base64
 import imp
@@ -116,8 +115,6 @@
 import spack.error
 import spack.compilers as compilers
 
-# TODO: move display_specs to some other location.
-from spack.cmd.find import display_specs
 from spack.version import *
 from spack.util.string import *
 from spack.util.prefix import Prefix
@@ -155,6 +152,7 @@
    every time we call str()"""
 _any_version = VersionList([':'])
 
+# Special types of dependencies.
 alldeps = ('build', 'link', 'run')
 nolink = ('build', 'run')
 
@@ -296,10 +294,15 @@ def __repr__(self):
 
 @key_ordering
 class DependencySpec(object):
-    """
+    """Dependencies can be one (or more) of several types:
-    Dependencies have conditions in which they apply.
 
-    This stores both what is depended on and why it is a dependency.
+    - build: needs to be in the PATH at build time.
+    - link: is linked to and added to compiler flags.
+    - run: needs to be in the PATH for the package to run.
+
+    Fields:
+    - spec: the spack.spec.Spec description of a dependency.
+    - deptypes: strings representing the type of dependency this is.
     """
     def __init__(self, spec, deptypes):
         self.spec = spec
@@ -558,15 +561,15 @@ def dependents(self, deptype=None):
     def _find_deps_dict(self, where, deptype):
         deptype = self._deptype_norm(deptype)
 
-        return [(dep.spec.name, dep)
+        return dict((dep.spec.name, dep)
                     for dep in where.values()
-                if deptype and any(d in deptype for d in dep.deptypes)]
+                    if deptype and any(d in deptype for d in dep.deptypes))
 
     def dependencies_dict(self, deptype=None):
-        return dict(self._find_deps_dict(self._dependencies, deptype))
+        return self._find_deps_dict(self._dependencies, deptype)
 
     def dependents_dict(self, deptype=None):
-        return dict(self._find_deps_dict(self._dependents, deptype))
+        return self._find_deps_dict(self._dependents, deptype)
 
     #
     # Private routines here are called by the parser when building a spec.
@@ -644,7 +647,8 @@ def _set_platform(self, value):
                 mod = imp.load_source(mod_name, path)
                 class_name = mod_to_class(value)
                 if not hasattr(mod, class_name):
-                    tty.die('No class %s defined in %s' % (class_name, mod_name))
+                    tty.die(
+                        'No class %s defined in %s' % (class_name, mod_name))
                 cls = getattr(mod, class_name)
                 if not inspect.isclass(cls):
                     tty.die('%s.%s is not a class' % (mod_name, class_name))
@@ -667,13 +671,15 @@ def _set_platform(self, value):
 
     def _set_os(self, value):
         """Called by the parser to set the architecture operating system"""
-        if self.architecture.platform:
+        arch = self.architecture
-            self.architecture.platform_os = self.architecture.platform.operating_system(value)
+        if arch.platform:
+            arch.platform_os = arch.platform.operating_system(value)
 
     def _set_target(self, value):
         """Called by the parser to set the architecture target"""
-        if self.architecture.platform:
+        arch = self.architecture
-            self.architecture.target = self.architecture.platform.target(value)
+        if arch.platform:
+            arch.target = arch.platform.target(value)
 
     def _add_dependency(self, spec, deptypes):
         """Called by the parser to add another spec as a dependency."""
@@ -688,7 +694,8 @@ def _add_dependency(self, spec, deptypes):
     #
     @property
     def fullname(self):
-        return (('%s.%s' % (self.namespace, self.name)) if self.namespace else
+        return (
+            ('%s.%s' % (self.namespace, self.name)) if self.namespace else
             (self.name if self.name else ''))
 
     @property
@@ -745,15 +752,15 @@ def concrete(self):
         if self._concrete:
             return True
 
-        self._concrete = bool(not self.virtual
+        self._concrete = bool(not self.virtual and
-                              and self.namespace is not None
+                              self.namespace is not None and
-                              and self.versions.concrete
+                              self.versions.concrete and
-                              and self.variants.concrete
+                              self.variants.concrete and
-                              and self.architecture
+                              self.architecture and
-                              and self.architecture.concrete
+                              self.architecture.concrete and
-                              and self.compiler and self.compiler.concrete
+                              self.compiler and self.compiler.concrete and
-                              and self.compiler_flags.concrete
+                              self.compiler_flags.concrete and
-                              and self._dependencies.concrete)
+                              self._dependencies.concrete)
         return self._concrete
 
     def traverse(self, visited=None, deptype=None, **kwargs):
@@ -914,9 +921,11 @@ def to_node_dict(self):
         d = {
             'parameters': params,
             'arch': self.architecture,
-            'dependencies': dict((d, (deps[d].spec.dag_hash(),
+            'dependencies': dict(
-                                      deps[d].deptypes))
+                (name, {
-                                 for d in sorted(deps.keys()))
+                    'hash': dspec.spec.dag_hash(),
+                    'type': [str(s) for s in dspec.deptypes]})
+                for name, dspec in deps.items())
         }
 
         # Older concrete specs do not have a namespace.  Omit for
@@ -982,13 +991,33 @@ def from_node_dict(node):
             raise SpackRecordError(
                 "Did not find a valid format for variants in YAML file")
 
-        # XXX(deptypes): why are dependencies not meant to be read here?
+        # Don't read dependencies here; from_node_dict() is used by
-        #for name, dep_info in node['dependencies'].items():
+        # from_yaml() to read the root *and* each dependency spec.
-        #    (dag_hash, deptypes) = dep_info
-        #    spec._dependencies[name] = DependencySpec(dag_hash, deptypes)
 
         return spec
 
+    @staticmethod
+    def read_yaml_dep_specs(dependency_dict):
+        """Read the DependencySpec portion of a YAML-formatted Spec.
+
+        This needs to be backward-compatible with older spack spec
+        formats so that reindex will work on old specs/databases.
+        """
+        for dep_name, elt in dependency_dict.items():
+            if isinstance(elt, basestring):
+                # original format, elt is just the dependency hash.
+                dag_hash, deptypes = elt, ['build', 'link']
+            elif isinstance(elt, tuple):
+                # original deptypes format: (used tuples, not future-proof)
+                dag_hash, deptypes = elt
+            elif isinstance(elt, dict):
+                # new format: elements of dependency spec are keyed.
+                dag_hash, deptypes = elt['hash'], elt['type']
+            else:
+                raise SpecError("Couldn't parse dependency types in spec.")
+
+            yield dep_name, dag_hash, list(deptypes)
+
     @staticmethod
     def from_yaml(stream):
         """Construct a spec from YAML.
@@ -1000,27 +1029,30 @@ def from_yaml(stream):
         represent more than the DAG does.
 
         """
-        deps = {}
-        spec = None
-
         try:
             yfile = yaml.load(stream)
         except MarkedYAMLError, e:
             raise SpackYAMLError("error parsing YAML spec:", str(e))
 
-        for node in yfile['spec']:
+        nodes = yfile['spec']
-            name = next(iter(node))
-            dep = Spec.from_node_dict(node)
-            if not spec:
-                spec = dep
-            deps[dep.name] = dep
 
-        for node in yfile['spec']:
+        # Read nodes out of list.  Root spec is the first element;
+        # dependencies are the following elements.
+        dep_list = [Spec.from_node_dict(node) for node in nodes]
+        if not dep_list:
+            raise SpecError("YAML spec contains no nodes.")
+        deps = dict((spec.name, spec) for spec in dep_list)
+        spec = dep_list[0]
+
+        for node in nodes:
+            # get dependency dict from the node.
             name = next(iter(node))
-            for dep_name, (dep, deptypes) in \
+            yaml_deps = node[name]['dependencies']
-                    node[name]['dependencies'].items():
+            for dname, dhash, dtypes in Spec.read_yaml_dep_specs(yaml_deps):
-                deps[name]._dependencies[dep_name] = \
+                # Fill in dependencies by looking them up by name in deps dict
-                        DependencySpec(deps[dep_name], deptypes)
+                deps[name]._dependencies[dname] = DependencySpec(
+                    deps[dname], set(dtypes))
+
         return spec
 
     def _concretize_helper(self, presets=None, visited=None):
@@ -1171,14 +1203,16 @@ def _expand_virtual_packages(self):
                 def feq(cfield, sfield):
                     return (not cfield) or (cfield == sfield)
 
-                if replacement is spec or (feq(replacement.name, spec.name) and
+                if replacement is spec or (
+                        feq(replacement.name, spec.name) and
                         feq(replacement.versions, spec.versions) and
                         feq(replacement.compiler, spec.compiler) and
                         feq(replacement.architecture, spec.architecture) and
                         feq(replacement._dependencies, spec._dependencies) and
                         feq(replacement.variants, spec.variants) and
                         feq(replacement.external, spec.external) and
-                    feq(replacement.external_module, spec.external_module)):
+                        feq(replacement.external_module,
+                            spec.external_module)):
                     continue
                 # Refine this spec to the candidate. This uses
                 # replace_with AND dup so that it can work in
@@ -1235,10 +1269,10 @@ def concretize(self):
             if s.namespace is None:
                 s.namespace = spack.repo.repo_for_pkg(s.name).namespace
 
-
         for s in self.traverse(root=False):
             if s.external_module:
-                compiler = spack.compilers.compiler_for_spec(s.compiler, s.architecture)
+                compiler = spack.compilers.compiler_for_spec(
+                    s.compiler, s.architecture)
                 for mod in compiler.modules:
                     load_module(mod)
 
@@ -1505,13 +1539,13 @@ def normalize(self, force=False):
         # Ensure first that all packages & compilers in the DAG exist.
         self.validate_names()
         # Get all the dependencies into one DependencyMap
-        spec_deps = self.flat_dependencies_with_deptype(copy=False,
+        spec_deps = self.flat_dependencies_with_deptype(
-                                                        deptype_query=alldeps)
+            copy=False, deptype_query=alldeps)
 
         # Initialize index of virtual dependency providers if
         # concretize didn't pass us one already
-        provider_index = ProviderIndex([s.spec for s in spec_deps.values()],
+        provider_index = ProviderIndex(
-                                       restrict=True)
+            [s.spec for s in spec_deps.values()], restrict=True)
 
         # traverse the package DAG and fill out dependencies according
         # to package files & their 'when' specs
@@ -1584,20 +1618,17 @@ def constrain(self, other, deps=True):
                                                     other.variants[v])
 
         # TODO: Check out the logic here
-        if self.architecture is not None and other.architecture is not None:
+        sarch, oarch = self.architecture, other.architecture
-            if self.architecture.platform is not None and other.architecture.platform is not None:
+        if sarch is not None and oarch is not None:
-                if self.architecture.platform != other.architecture.platform:
+            if sarch.platform is not None and oarch.platform is not None:
-                    raise UnsatisfiableArchitectureSpecError(self.architecture,
+                if sarch.platform != oarch.platform:
-                                                             other.architecture)
+                    raise UnsatisfiableArchitectureSpecError(sarch, oarch)
-            if self.architecture.platform_os is not None and other.architecture.platform_os is not None:
+            if sarch.platform_os is not None and oarch.platform_os is not None:
-                if self.architecture.platform_os != other.architecture.platform_os:
+                if sarch.platform_os != oarch.platform_os:
-                    raise UnsatisfiableArchitectureSpecError(self.architecture,
+                    raise UnsatisfiableArchitectureSpecError(sarch, oarch)
-                                                             other.architecture)
+            if sarch.target is not None and oarch.target is not None:
-            if self.architecture.target is not None and other.architecture.target is not None:
+                if sarch.target != oarch.target:
-                if self.architecture.target != other.architecture.target:
+                    raise UnsatisfiableArchitectureSpecError(sarch, oarch)
-                    raise UnsatisfiableArchitectureSpecError(self.architecture,
-                                                             other.architecture)
-
 
         changed = False
         if self.compiler is not None and other.compiler is not None:
@@ -1612,15 +1643,16 @@ def constrain(self, other, deps=True):
         changed |= self.compiler_flags.constrain(other.compiler_flags)
 
         old = str(self.architecture)
-        if self.architecture is None or other.architecture is None:
+        sarch, oarch = self.architecture, other.architecture
-            self.architecture = self.architecture or other.architecture
+        if sarch is None or other.architecture is None:
+            self.architecture = sarch or oarch
         else:
-            if self.architecture.platform is None or other.architecture.platform is None:
+            if sarch.platform is None or oarch.platform is None:
-                self.architecture.platform = self.architecture.platform or other.architecture.platform
+                self.architecture.platform = sarch.platform or oarch.platform
-            if self.architecture.platform_os is None or other.architecture.platform_os is None:
+            if sarch.platform_os is None or oarch.platform_os is None:
-                self.architecture.platform_os = self.architecture.platform_os or other.architecture.platform_os
+                sarch.platform_os = sarch.platform_os or oarch.platform_os
-            if self.architecture.target is None or other.architecture.target is None:
+            if sarch.target is None or oarch.target is None:
-                self.architecture.target = self.architecture.target or other.architecture.target
+                sarch.target = sarch.target or oarch.target
         changed |= (str(self.architecture) != old)
 
         if deps:
@@ -1751,15 +1783,25 @@ def satisfies(self, other, deps=True, strict=False):
 
         # Architecture satisfaction is currently just string equality.
         # If not strict, None means unconstrained.
-        if self.architecture and other.architecture:
+        sarch, oarch = self.architecture, other.architecture
-            if ((self.architecture.platform and other.architecture.platform and self.architecture.platform != other.architecture.platform) or
+        if sarch and oarch:
-                (self.architecture.platform_os and other.architecture.platform_os and self.architecture.platform_os != other.architecture.platform_os) or
+            if ((sarch.platform and
-                (self.architecture.target and other.architecture.target and self.architecture.target != other.architecture.target)):
+                 oarch.platform and
+                 sarch.platform != oarch.platform) or
+
+                (sarch.platform_os and
+                 oarch.platform_os and
+                 sarch.platform_os != oarch.platform_os) or
+
+                (sarch.target and
+                 oarch.target and
+                 sarch.target != oarch.target)):
                 return False
-        elif strict and ((other.architecture and not self.architecture) or
+
-                         (other.architecture.platform and not self.architecture.platform) or
+        elif strict and ((oarch and not sarch) or
-                         (other.architecture.platform_os and not self.architecture.platform_os) or
+                         (oarch.platform and not sarch.platform) or
-                         (other.architecture.target and not self.architecture.target)):
+                         (oarch.platform_os and not sarch.platform_os) or
+                         (oarch.target and not sarch.target)):
             return False
 
         if not self.compiler_flags.satisfies(
@@ -1841,11 +1883,16 @@ def _dup(self, other, **kwargs):
         # We don't count dependencies as changes here
         changed = True
         if hasattr(self, 'name'):
-            changed = (self.name != other.name and self.versions != other.versions and \
+            changed = (self.name != other.name and
-                       self.architecture != other.architecture and self.compiler != other.compiler and \
+                       self.versions != other.versions and
-                       self.variants != other.variants and self._normal != other._normal and \
+                       self.architecture != other.architecture and
-                       self.concrete != other.concrete and self.external != other.external and \
+                       self.compiler != other.compiler and
-                       self.external_module != other.external_module and self.compiler_flags != other.compiler_flags)
+                       self.variants != other.variants and
+                       self._normal != other._normal and
+                       self.concrete != other.concrete and
+                       self.external != other.external and
+                       self.external_module != other.external_module and
+                       self.compiler_flags != other.compiler_flags)
 
         # Local node attributes get copied first.
         self.name = other.name
@@ -2000,7 +2047,6 @@ def _cmp_node(self):
                 self.compiler,
                 self.compiler_flags)
 
-
     def eq_node(self, other):
         """Equality with another spec, not including dependencies."""
         return self._cmp_node() == other._cmp_node()
@@ -2196,41 +2242,39 @@ def write(s, c):
     def dep_string(self):
         return ''.join("^" + dep.format() for dep in self.sorted_deps())
 
-
     def __cmp__(self, other):
-        #Package name sort order is not configurable, always goes alphabetical
+        # Package name sort order is not configurable, always goes alphabetical
         if self.name != other.name:
             return cmp(self.name, other.name)
 
-        #Package version is second in compare order
+        # Package version is second in compare order
         pkgname = self.name
         if self.versions != other.versions:
-            return spack.pkgsort.version_compare(pkgname,
+            return spack.pkgsort.version_compare(
-                         self.versions, other.versions)
+                pkgname, self.versions, other.versions)
 
-        #Compiler is third
+        # Compiler is third
         if self.compiler != other.compiler:
-            return spack.pkgsort.compiler_compare(pkgname,
+            return spack.pkgsort.compiler_compare(
-                         self.compiler, other.compiler)
+                pkgname, self.compiler, other.compiler)
 
-        #Variants
+        # Variants
         if self.variants != other.variants:
-            return spack.pkgsort.variant_compare(pkgname,
+            return spack.pkgsort.variant_compare(
-                         self.variants, other.variants)
+                pkgname, self.variants, other.variants)
 
-        #Target
+        # Target
         if self.architecture != other.architecture:
-            return spack.pkgsort.architecture_compare(pkgname,
+            return spack.pkgsort.architecture_compare(
-                         self.architecture, other.architecture)
+                pkgname, self.architecture, other.architecture)
 
-        #Dependency is not configurable
+        # Dependency is not configurable
         if self._dependencies != other._dependencies:
             return -1 if self._dependencies < other._dependencies else 1
 
-        #Equal specs
+        # Equal specs
         return 0
 
-
     def __str__(self):
         return self.format() + self.dep_string()
 
@@ -2244,12 +2288,14 @@ def tree(self, **kwargs):
         indent = kwargs.pop('indent', 0)
         fmt = kwargs.pop('format', '$_$@$%@+$+$=')
         prefix = kwargs.pop('prefix', None)
+        deptypes = kwargs.pop('deptypes', ('build', 'link'))
         check_kwargs(kwargs, self.tree)
 
         out = ""
         cur_id = 0
         ids = {}
-        for d, node in self.traverse(order='pre', cover=cover, depth=True):
+        for d, node in self.traverse(
+                order='pre', cover=cover, depth=True, deptypes=deptypes):
             if prefix is not None:
                 out += prefix(node)
             out += " " * indent
@@ -2303,8 +2349,8 @@ def __init__(self):
 # Lexer is always the same for every parser.
 _lexer = SpecLexer()
 
-class SpecParser(spack.parse.Parser):
 
+class SpecParser(spack.parse.Parser):
     def __init__(self):
         super(SpecParser, self).__init__(_lexer)
         self.previous = None
@@ -2357,8 +2403,8 @@ def do_parse(self):
         except spack.parse.ParseError, e:
             raise SpecParseError(e)
 
-
+        # If the spec has an os or a target and no platform, give it
-        # If the spec has an os or a target and no platform, give it the default platform
+        # the default platform
         for spec in specs:
             for s in spec.traverse():
                 if s.architecture.os_string or s.architecture.target_string:

lib/spack/spack/test/architecture.py

@@ -1,7 +1,31 @@
+##############################################################################
+# 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
+##############################################################################
 """ Test checks if the architecture class is created correctly and also that
     the functions are looking for the correct architecture name
 """
-import unittest
+import itertools
 import os
 import platform as py_platform
 import spack
@@ -14,9 +38,8 @@
 
 from spack.test.mock_packages_test import *
 
-#class ArchitectureTest(unittest.TestCase):
-class ArchitectureTest(MockPackagesTest):
 
+class ArchitectureTest(MockPackagesTest):
     def setUp(self):
         super(ArchitectureTest, self).setUp()
         self.platform = spack.architecture.platform()
@@ -36,24 +59,22 @@ def test_dict_functions_for_architecture(self):
 
         self.assertEqual(arch, new_arch)
 
-        self.assertTrue( isinstance(arch, spack.architecture.Arch) )
+        self.assertTrue(isinstance(arch, spack.architecture.Arch))
-        self.assertTrue( isinstance(arch.platform, spack.architecture.Platform) )
+        self.assertTrue(isinstance(arch.platform, spack.architecture.Platform))
-        self.assertTrue( isinstance(arch.platform_os,
+        self.assertTrue(isinstance(arch.platform_os,
-                                    spack.architecture.OperatingSystem) )
+                                   spack.architecture.OperatingSystem))
-        self.assertTrue( isinstance(arch.target,
+        self.assertTrue(isinstance(arch.target,
-                                    spack.architecture.Target) )
+                                   spack.architecture.Target))
-        self.assertTrue( isinstance(new_arch, spack.architecture.Arch) )
+        self.assertTrue(isinstance(new_arch, spack.architecture.Arch))
-        self.assertTrue( isinstance(new_arch.platform,
+        self.assertTrue(isinstance(new_arch.platform,
-                                    spack.architecture.Platform) )
+                                   spack.architecture.Platform))
-        self.assertTrue( isinstance(new_arch.platform_os,
+        self.assertTrue(isinstance(new_arch.platform_os,
-                                    spack.architecture.OperatingSystem) )
+                                   spack.architecture.OperatingSystem))
-        self.assertTrue( isinstance(new_arch.target,
+        self.assertTrue(isinstance(new_arch.target,
-                                    spack.architecture.Target) )
+                                   spack.architecture.Target))
-
 
     def test_platform(self):
         output_platform_class = spack.architecture.platform()
-        my_arch_class = None
         if os.path.exists('/opt/cray/craype'):
             my_platform_class = CrayXc()
         elif os.path.exists('/bgsys'):
@@ -107,10 +128,11 @@ def test_user_input_combination(self):
         combinations = itertools.product(os_list, target_list)
         results = []
         for arch in combinations:
-            o,t = arch
+            o, t = arch
             spec = Spec("libelf os=%s target=%s" % (o, t))
             spec.concretize()
-            results.append(spec.architecture.platform_os == self.platform.operating_system(o))
+            results.append(spec.architecture.platform_os ==
+                           self.platform.operating_system(o))
             results.append(spec.architecture.target == self.platform.target(t))
         res = all(results)
 

share/spack/qa/run-flake8

@@ -18,7 +18,7 @@ if [[ ! $flake8 ]]; then
 fi
 
 # Check if changed files are flake8 conformant [framework]
-changed=$(git diff --name-only develop... | grep '.py$')
+changed=$(git diff --name-only --find-renames develop... | grep '.py$')
 
 # Add approved style exemptions to the changed packages.
 for file in $changed; do
@@ -26,6 +26,7 @@ for file in $changed; do
         cp "$file" "$file~"
 
         # Exempt lines with urls and descriptions from overlong line errors.
+        perl -i -pe 's/^(\s*homepage\s*=.*)$/\1  # NOQA: ignore=E501/' $file
         perl -i -pe 's/^(\s*url\s*=.*)$/\1  # NOQA: ignore=E501/' $file
         perl -i -pe 's/^(\s*version\(.*\).*)$/\1  # NOQA: ignore=E501/' $file
         perl -i -pe 's/^(\s*variant\(.*\).*)$/\1  # NOQA: ignore=E501/' $file

share/spack/setup-env.sh

@@ -57,6 +57,11 @@
 ########################################################################
 
 function spack {
+    # Zsh does not do word splitting by default, this enables it for this function only
+    if [ -n "$ZSH_VERSION" ]; then
+        emulate -L sh
+    fi
+
     # save raw arguments into an array before butchering them
     args=( "$@" )
 
@@ -93,11 +98,18 @@ function spack {
             ;;
         "use"|"unuse"|"load"|"unload")
             # Shift any other args for use off before parsing spec.
+            _sp_subcommand_args=""
             _sp_module_args=""
-            if [[ "$1" =~ ^- ]]; then
+            while [[ "$1" =~ ^- ]]; do
-                _sp_module_args="$1"; shift
+                if [ "$1" = "-r" -o "$1" = "--dependencies" ]; then
-                _sp_spec="$@"
+                    _sp_subcommand_args="$_sp_subcommand_args $1"
+                else
+                    _sp_module_args="$_sp_module_args $1"
                 fi
+                shift
+            done
+
+            _sp_spec="$@"
 
             # Here the user has run use or unuse with a spec.  Find a matching
             # spec using 'spack module find', then use the appropriate module
@@ -105,19 +117,19 @@ function spack {
             # If spack module command comes back with an error, do nothing.
             case $_sp_subcommand in
                 "use")
-                    if _sp_full_spec=$(command spack $_sp_flags module find --module-type dotkit $_sp_spec); then
+                    if _sp_full_spec=$(command spack $_sp_flags module find $_sp_subcommand_args --module-type dotkit $_sp_spec); then
                         use $_sp_module_args $_sp_full_spec
                     fi ;;
                 "unuse")
-                    if _sp_full_spec=$(command spack $_sp_flags module find --module-type dotkit $_sp_spec); then
+                    if _sp_full_spec=$(command spack $_sp_flags module find $_sp_subcommand_args --module-type dotkit $_sp_spec); then
                         unuse $_sp_module_args $_sp_full_spec
                     fi ;;
                 "load")
-                    if _sp_full_spec=$(command spack $_sp_flags module find --module-type tcl $_sp_spec); then
+                    if _sp_full_spec=$(command spack $_sp_flags module find $_sp_subcommand_args --module-type tcl $_sp_spec); then
                         module load $_sp_module_args $_sp_full_spec
                     fi ;;
                 "unload")
-                    if _sp_full_spec=$(command spack $_sp_flags module find --module-type tcl $_sp_spec); then
+                    if _sp_full_spec=$(command spack $_sp_flags module find $_sp_subcommand_args --module-type tcl $_sp_spec); then
                         module unload $_sp_module_args $_sp_full_spec
                     fi ;;
             esac

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

@@ -0,0 +1,53 @@
+##############################################################################
+# 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 Gts(Package):
+    """GTS stands for the GNU Triangulated Surface Library.
+
+    It is an Open Source Free Software Library intended to provide a set of
+    useful functions to deal with 3D surfaces meshed with interconnected
+    triangles. The source code is available free of charge under the Free
+    Software LGPL license.
+
+    The code is written entirely in C with an object-oriented approach
+    based mostly on the design of GTK+. Careful attention is paid to
+    performance related issues as the initial goal of GTS is to provide a
+    simple and efficient library to scientists dealing with 3D computational
+    surface meshes.
+    """
+
+    homepage = "http://gts.sourceforge.net/index.html"
+    url = "http://gts.sourceforge.net/tarballs/gts-snapshot-121130.tar.gz"
+
+    version('121130', '023ebb6b13b8707534182a3ef0d12908')
+
+    depends_on('glib')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+        make()
+        make('install')

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

@@ -0,0 +1,76 @@
+##############################################################################
+# 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 Hmmer(Package):
+    """HMMER is used for searching sequence databases for sequence homologs,
+    and for making sequence alignments. It implements methods using
+    probabilistic models called profile hidden Markov models (profile HMMs).
+    """
+    homepage = 'http://www.hmmer.org'
+    url      = 'http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz'
+
+    version('3.1b2', 'c8c141018bc0ccd7fc37b33f2b945d5f')
+    version('3.0',   '4cf685f3bc524ba5b5cdaaa070a83588')
+    version('2.4i',  'dab234c87e026ac1de942450750acd20')
+    version('2.3.2', '5f073340c0cf761288f961a73821228a')
+    version('2.3.1', 'c724413e5761c630892506698a4716e2')
+
+    variant('mpi', default=True,  description='Compile with MPI')
+    variant('gsl', default=False, description='Compile with GSL')
+
+    depends_on('mpi', when='+mpi')
+    depends_on('gsl', when='+gsl')
+
+    def url_for_version(self, version):
+        base_url = 'http://eddylab.org/software'
+
+        if version >= Version('3.0'):
+            return '{0}/hmmer3/{1}/hmmer-{1}.tar.gz'.format(base_url, version)
+        else:
+            return '{0}/hmmer/{1}/hmmer-{1}.tar.gz'.format(base_url, version)
+
+    def install(self, spec, prefix):
+        configure_args = [
+            '--prefix={0}'.format(prefix)
+        ]
+
+        if '+gsl' in self.spec:
+            configure_args.extend([
+                '--with-gsl',
+                'LIBS=-lgsl -lgslcblas'
+            ])
+
+        if '+mpi' in self.spec:
+            configure_args.append('--enable-mpi')
+
+        configure(*configure_args)
+        make()
+
+        if self.run_tests:
+            make('check')
+
+        make('install')

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

@@ -23,7 +23,9 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os, sys
+import os
+import sys
+
 
 class Hypre(Package):
     """Hypre is a library of high performance preconditioners that
@@ -37,7 +39,7 @@ class Hypre(Package):
     version('2.10.0b', '768be38793a35bb5d055905b271f5b8e')
 
     # hypre does not know how to build shared libraries on Darwin
-    variant('shared', default=sys.platform!='darwin', description="Build shared library version (disables static library)")
+    variant('shared', default=(sys.platform != 'darwin'), description="Build shared library version (disables static library)")
     # SuperluDist have conflicting headers with those in Hypre
     variant('internal-superlu', default=True, description="Use internal Superlu routines")
 
@@ -46,21 +48,26 @@ class Hypre(Package):
     depends_on("lapack")
 
     def install(self, spec, prefix):
-        blas_dir = spec['blas'].prefix
+        os.environ['CC'] = spec['mpi'].mpicc
-        lapack_dir = spec['lapack'].prefix
+        os.environ['CXX'] = spec['mpi'].mpicxx
-        mpi_dir = spec['mpi'].prefix
+        os.environ['F77'] = spec['mpi'].mpif77
-
-        os.environ['CC'] = os.path.join(mpi_dir, 'bin', 'mpicc')
-        os.environ['CXX'] = os.path.join(mpi_dir, 'bin', 'mpicxx')
-        os.environ['F77'] = os.path.join(mpi_dir, 'bin', 'mpif77')
-
 
+        # Since +shared does not build on macOS and also Atlas does not have
+        # a single static lib to build against, link against shared libs with
+        # a hope that --whole-archive linker option (or alike) was used
+        # to command the linker to include whole static libs' content into the
+        # shared lib
+        # Note: --with-(lapack|blas)_libs= needs space separated list of names
         configure_args = [
-                "--prefix=%s" % prefix,
+            '--prefix=%s' % prefix,
-                "--with-lapack-libs=lapack",
+            '--with-lapack-libs=%s' % to_lib_name(
-                "--with-lapack-lib-dirs=%s/lib" % lapack_dir,
+                spec['lapack'].lapack_shared_lib),
-                "--with-blas-libs=blas",
+            '--with-lapack-lib-dirs=%s/lib' % spec['lapack'].prefix,
-                "--with-blas-lib-dirs=%s/lib" % blas_dir]
+            '--with-blas-libs=%s' % to_lib_name(
+                spec['blas'].blas_shared_lib),
+            '--with-blas-lib-dirs=%s/lib' % spec['blas'].prefix
+        ]
+
         if '+shared' in self.spec:
             configure_args.append("--enable-shared")
 
@@ -76,4 +83,12 @@ def install(self, spec, prefix):
             configure(*configure_args)
 
             make()
+            if self.run_tests:
+                make("check")
+                make("test")
+                Executable(join_path('test', 'ij'))()
+                sstruct = Executable(join_path('test', 'struct'))
+                sstruct()
+                sstruct('-in', 'test/sstruct.in.default', '-solver', '40',
+                        '-rhsone')
             make("install")

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

@@ -63,6 +63,7 @@ class Openmpi(Package):
     list_url = "http://www.open-mpi.org/software/ompi/"
     list_depth = 3
 
+    version('2.0.0', 'cdacc800cb4ce690c1f1273cb6366674')
     version('1.10.3', 'e2fe4513200e2aaa1500b762342c674b')
     version('1.10.2', 'b2f43d9635d2d52826e5ef9feb97fd4c')
     version('1.10.1', 'f0fcd77ed345b7eafb431968124ba16e')
@@ -101,6 +102,7 @@ class Openmpi(Package):
 
     provides('mpi@:2.2', when='@1.6.5')
     provides('mpi@:3.0', when='@1.7.5:')
+    provides('mpi@:3.1', when='@2.0.0:')
 
     depends_on('hwloc')
     depends_on('sqlite', when='+sqlite3')
@@ -169,7 +171,8 @@ def install(self, spec, prefix):
             '--with-psm2' if '+psm2' in spec else '--without-psm2',
             '--with-mxm' if '+mxm' in spec else '--without-mxm',
             # Other options
-            '--enable-mpi-thread-multiple' if '+thread_multiple' in spec else '--disable-mpi-thread-multiple',  # NOQA: ignore=E501
+            ('--enable-mpi-thread-multiple' if '+thread_multiple' in spec
+                else '--disable-mpi-thread-multiple'),
             '--with-pmi' if '+pmi' in spec else '--without-pmi',
             '--with-sqlite3' if '+sqlite3' in spec else '--without-sqlite3',
             '--enable-vt' if '+vt' in spec else '--disable-vt'

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

@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyNumpy(Package):
     """NumPy is the fundamental package for scientific computing with Python.
     It contains among other things: a powerful N-dimensional array object,
@@ -38,7 +39,6 @@ class PyNumpy(Package):
     version('1.9.2',  'a1ed53432dbcd256398898d35bc8e645')
     version('1.9.1',  '78842b73560ec378142665e712ae4ad9')
 
-
     variant('blas',   default=True)
     variant('lapack', default=True)
 
@@ -63,6 +63,6 @@ def install(self, spec, prefix):
                 f.write('[DEFAULT]\n')
                 f.write('libraries=%s\n'    % ','.join(libraries))
                 f.write('library_dirs=%s\n' % ':'.join(library_dirs))
+                f.write('rpath=%s\n' % ':'.join(library_dirs))
 
         python('setup.py', 'install', '--prefix=%s' % prefix)
-

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

@@ -38,16 +38,29 @@ class Python(Package):
     homepage = "http://www.python.org"
     url      = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz"
 
+    version('3.5.2', '3fe8434643a78630c61c6464fe2e7e72')
     version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe')
     version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36')
-    version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True)
+    version('3.4.3', '4281ff86778db65892c05151d5de738d')
+    version('3.3.6', 'cdb3cd08f96f074b3f3994ccb51063e9')
+    version('3.2.6', '23815d82ae706e9b781ca65865353d39')
+    version('3.1.5', '02196d3fc7bc76bdda68aa36b0dd16ab')
+    version('2.7.12', '88d61f82e3616a4be952828b3694109d', preferred=True)
+    version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b')
     version('2.7.10', 'd7547558fd673bd9d38e2108c6b42521')
     version('2.7.9', '5eebcaa0030dc4061156d3429657fb83')
     version('2.7.8', 'd4bca0159acb0b44a781292b5231936f')
 
     extendable = True
 
-    variant('ucs4', default=False, description='Enable UCS4 unicode strings')
+    variant('ucs4', default=False, description='Enable UCS4 (wide) unicode strings')
+    # From https://docs.python.org/2/c-api/unicode.html: Python's default
+    # builds use a 16-bit type for Py_UNICODE and store Unicode values
+    # internally as UCS2. It is also possible to build a UCS4 version of Python
+    # (most recent Linux distributions come with UCS4 builds of Python).  These
+    # builds then use a 32-bit type for Py_UNICODE and store Unicode data
+    # internally as UCS4. Note that UCS2 and UCS4 Python builds are not binary
+    # compatible.
 
     depends_on("openssl")
     depends_on("bzip2")
@@ -85,7 +98,13 @@ def install(self, spec, prefix):
         ]
 
         if '+ucs4' in spec:
+            if spec.satisfies('@:2.7'):
                 config_args.append('--enable-unicode=ucs4')
+            elif spec.satisfies('@3.0:3.2'):
+                config_args.append('--with-wide-unicode')
+            elif spec.satisfies('@3.3:'):
+                # https://docs.python.org/3.3/whatsnew/3.3.html
+                raise ValueError('+ucs4 variant not compatible with Python 3.3 and beyond')  # NOQA: ignore=E501
 
         if spec.satisfies('@3:'):
             config_args.append('--without-ensurepip')

var/spack/repos/builtin/packages/r-ggvis/package.py

@@ -0,0 +1,51 @@
+##############################################################################
+# 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 RGgvis(Package):
+    """An implementation of an interactive grammar of graphics, taking the best
+    parts of 'ggplot2', combining them with the reactive framework from 'shiny'
+    and web graphics from 'vega'."""
+
+    homepage = "http://ggvis.rstudio.com/"
+    url      = "https://cran.r-project.org/src/contrib/ggvis_0.4.2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/ggvis"
+
+    version('0.4.2', '039f45e5c7f1e0652779163d7d99f922')
+
+    extends('R')
+
+    depends_on('r-assertthat')
+    depends_on('r-jsonlite')
+    depends_on('r-shiny')
+    depends_on('r-magrittr')
+    depends_on('r-dplyr')
+    depends_on('r-lazyeval')
+    depends_on('r-htmltools')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-htmltools/package.py

@@ -0,0 +1,44 @@
+##############################################################################
+# 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 RHtmltools(Package):
+    """Tools for HTML generation and output."""
+
+    homepage = "https://github.com/rstudio/htmltools"
+    url      = "https://cran.r-project.org/src/contrib/htmltools_0.3.5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/htmltools"
+
+    version('0.3.5', '5f001aff4a39e329f7342dcec5139724')
+
+    extends('R')
+
+    depends_on('r-digest')
+    depends_on('r-rcpp')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-httpuv/package.py

@@ -0,0 +1,49 @@
+##############################################################################
+# 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 RHttpuv(Package):
+    """Provides low-level socket and protocol support for handling HTTP and
+    WebSocket requests directly from within R. It is primarily intended as a
+    building block for other packages, rather than making it particularly easy
+    to create complete web applications using httpuv alone. httpuv is built on
+    top of the libuv and http-parser C libraries, both of which were developed
+    by Joyent, Inc. (See LICENSE file for libuv and http-parser license
+    information.)"""
+
+    homepage = "https://github.com/rstudio/httpuv"
+    url      = "https://cran.r-project.org/src/contrib/httpuv_1.3.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/httpuv"
+
+    version('1.3.3', 'c78ae068cf59e949b9791be987bb4489')
+
+    extends('R')
+
+    depends_on('r-rcpp')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-shiny/package.py

@@ -0,0 +1,52 @@
+##############################################################################
+# 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 RShiny(Package):
+    """Makes it incredibly easy to build interactive web applications with R.
+    Automatic "reactive" binding between inputs and outputs and extensive
+    pre-built widgets make it possible to build beautiful, responsive, and
+    powerful applications with minimal effort."""
+
+    homepage = "http://shiny.rstudio.com/"
+    url      = "https://cran.r-project.org/src/contrib/shiny_0.13.2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/shiny"
+
+    version('0.13.2', 'cb5bff7a28ad59ec2883cd0912ca9611')
+
+    extends('R')
+
+    depends_on('r-httpuv')
+    depends_on('r-mime')
+    depends_on('r-jsonlite')
+    depends_on('r-xtable')
+    depends_on('r-digest')
+    depends_on('r-htmltools')
+    depends_on('r-R6')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-xtable/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 RXtable(Package):
+    """Coerce data to LaTeX and HTML tables."""
+
+    homepage = "http://xtable.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/xtable_1.8-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/xtable"
+
+    version('1.8-2', '239e4825cd046156a67efae3aac01d86')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -71,6 +71,7 @@ def install(self, spec, prefix):
         # Configure and install
         options = ['--prefix=%s' % prefix,
                    '--enable-mpi' if '+mpi' in spec else '--disable-mpi',
+                   '--with-metis={0}'.format(spec['metis'].prefix),
                    '--enable-optimization']
         configure(*options)
         make()

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

@@ -118,6 +118,7 @@ def install(self, spec, prefix):
         options.extend(std_cmake_args)
 
         mpi_bin = spec['mpi'].prefix.bin
+        # Note: -DXYZ_LIBRARY_NAMES= needs semicolon separated list of names
         options.extend([
             '-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
             '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
@@ -131,10 +132,12 @@ def install(self, spec, prefix):
             '-DTPL_ENABLE_MPI:BOOL=ON',
             '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
             '-DTPL_ENABLE_BLAS=ON',
-            '-DBLAS_LIBRARY_NAMES=blas',  # FIXME: don't hardcode names
+            '-DBLAS_LIBRARY_NAMES=%s' % to_lib_name(
+                spec['blas'].blas_shared_lib),
             '-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib,
             '-DTPL_ENABLE_LAPACK=ON',
-            '-DLAPACK_LIBRARY_NAMES=lapack',
+            '-DLAPACK_LIBRARY_NAMES=%s' % to_lib_name(
+                spec['lapack'].lapack_shared_lib),
             '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix,
             '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
             '-DTrilinos_ENABLE_CXX11:BOOL=ON',