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

Conflicts:
	lib/spack/spack/package.py

.gitignore

@@ -1,11 +1,12 @@
 /var/spack/stage
 /var/spack/cache
 *.pyc
-/opt/
+/opt
 *~
 .DS_Store
 .idea
-/etc/spack/*
+/etc/spack/licenses
+/etc/spack/*.yaml
 /etc/spackconfig
 /share/spack/dotkit
 /share/spack/modules

etc/spack/defaults/modules.yaml

@@ -1,8 +1,17 @@
 # -------------------------------------------------------------------------
-# This is the default spack module files generation configuration.
+# This is the default configuration for Spack's module file generation.
 #
-# Changes to this file will affect all users of this spack install,
+# Settings here are versioned with Spack and are intended to provide
-# although users can override these settings in their ~/.spack/modules.yaml.
+# sensible defaults out of the box. Spack maintainers should edit this
+# file to keep it current.
+#
+# Users can override these settings by editing the following files.
+#
+# Per-spack-instance settings (overrides defaults):
+#   $SPACK_ROOT/etc/spack/modules.yaml
+#
+# Per-user settings (overrides default and site settings):
+#   ~/.spack/modules.yaml
 # -------------------------------------------------------------------------
 modules:
   enable:

etc/spack/defaults/packages.yaml

@@ -0,0 +1,21 @@
+# -------------------------------------------------------------------------
+# This file controls default concretization preferences for Spack.
+#
+# Settings here are versioned with Spack and are intended to provide
+# sensible defaults out of the box. Spack maintainers should edit this
+# file to keep it current.
+#
+# Users can override these settings by editing the following files.
+#
+# Per-spack-instance settings (overrides defaults):
+#   $SPACK_ROOT/etc/spack/packages.yaml
+#
+# Per-user settings (overrides default and site settings):
+#   ~/.spack/packages.yaml
+# -------------------------------------------------------------------------
+packages:
+  all:
+    providers:
+      mpi: [openmpi, mpich]
+      blas: [openblas]
+      lapack: [openblas]

etc/spack/defaults/repos.yaml

@@ -0,0 +1,14 @@
+# -------------------------------------------------------------------------
+# This is the default spack repository configuration. It includes the
+# builtin spack package repository.
+#
+# Users can override these settings by editing the following files.
+#
+# Per-spack-instance settings (overrides defaults):
+#   $SPACK_ROOT/etc/spack/repos.yaml
+#
+# Per-user settings (overrides default and site settings):
+#   ~/.spack/repos.yaml
+# -------------------------------------------------------------------------
+repos:
+  - $spack/var/spack/repos/builtin

etc/spack/repos.yaml

@@ -1,8 +0,0 @@
-# -------------------------------------------------------------------------
-# This is the default spack repository configuration.
-#
-# Changes to this file will affect all users of this spack install,
-# although users can override these settings in their ~/.spack/repos.yaml.
-# -------------------------------------------------------------------------
-repos:
-  - $spack/var/spack/repos/builtin

lib/spack/env/cc

@@ -110,13 +110,13 @@ case "$command" in
         comp="CXX"
         lang_flags=CXX
         ;;
-    f90|fc|f95|gfortran|ifort|pgfortran|xlf90|nagfor)
+    ftn|f90|fc|f95|gfortran|ifort|pgfortran|xlf90|nagfor)
         command="$SPACK_FC"
         language="Fortran 90"
         comp="FC"
         lang_flags=F
         ;;
-    f77|gfortran|ifort|pgfortran|xlf|nagfor)
+    f77|gfortran|ifort|pgfortran|xlf|nagfor|ftn)
         command="$SPACK_F77"
         language="Fortran 77"
         comp="F77"

lib/spack/env/craype/CC

@@ -0,0 +1 @@
+../cc

lib/spack/env/craype/cc

@@ -0,0 +1 @@
+../cc

lib/spack/env/craype/ftn

@@ -0,0 +1 @@
+../cc

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/__init__.py

@@ -27,16 +27,18 @@
 import sys
 
 import llnl.util.tty as tty
-from llnl.util.lang import attr_setdefault
-
 import spack
-import spack.spec
 import spack.config
+import spack.spec
+from llnl.util.lang import *
+from llnl.util.tty.colify import *
+from llnl.util.tty.color import *
 
 #
 # Settings for commands that modify configuration
 #
-# Commands that modify confguration By default modify the *highest* priority scope.
+# Commands that modify confguration By default modify the *highest*
+# priority scope.
 default_modify_scope = spack.config.highest_precedence_scope().name
 # Commands that list confguration list *all* scopes by default.
 default_list_scope = None
@@ -107,11 +109,11 @@ def parse_specs(args, **kwargs):
 
         return specs
 
-    except spack.parse.ParseError, e:
+    except spack.parse.ParseError as e:
         tty.error(e.message, e.string, e.pos * " " + "^")
         sys.exit(1)
 
-    except spack.spec.SpecError, e:
+    except spack.spec.SpecError as e:
         tty.error(e.message)
         sys.exit(1)
 
@@ -145,3 +147,97 @@ def disambiguate_spec(spec):
         tty.die(*args)
 
     return matching_specs[0]
+
+
+def ask_for_confirmation(message):
+    while True:
+        tty.msg(message + '[y/n]')
+        choice = raw_input().lower()
+        if choice == 'y':
+            break
+        elif choice == 'n':
+            raise SystemExit('Operation aborted')
+        tty.warn('Please reply either "y" or "n"')
+
+
+def gray_hash(spec, length):
+    return colorize('@K{%s}' % spec.dag_hash(length))
+
+
+def display_specs(specs, **kwargs):
+    mode = kwargs.get('mode', 'short')
+    hashes = kwargs.get('long', False)
+    namespace = kwargs.get('namespace', False)
+    flags = kwargs.get('show_flags', False)
+    variants = kwargs.get('variants', False)
+
+    hlen = 7
+    if kwargs.get('very_long', False):
+        hashes = True
+        hlen = None
+
+    nfmt = '.' if namespace else '_'
+    ffmt = '$%+' if flags else ''
+    vfmt = '$+' if variants else ''
+    format_string = '$%s$@%s%s' % (nfmt, ffmt, vfmt)
+
+    # Make a dict with specs keyed by architecture and compiler.
+    index = index_by(specs, ('architecture', 'compiler'))
+
+    # Traverse the index and print out each package
+    for i, (architecture, compiler) in enumerate(sorted(index)):
+        if i > 0:
+            print
+
+        header = "%s{%s} / %s{%s}" % (spack.spec.architecture_color,
+                                      architecture, spack.spec.compiler_color,
+                                      compiler)
+        tty.hline(colorize(header), char='-')
+
+        specs = index[(architecture, compiler)]
+        specs.sort()
+
+        abbreviated = [s.format(format_string, color=True) for s in specs]
+        if mode == 'paths':
+            # Print one spec per line along with prefix path
+            width = max(len(s) for s in abbreviated)
+            width += 2
+            format = "    %%-%ds%%s" % width
+
+            for abbrv, spec in zip(abbreviated, specs):
+                if hashes:
+                    print(gray_hash(spec, hlen), )
+                print(format % (abbrv, spec.prefix))
+
+        elif mode == 'deps':
+            for spec in specs:
+                print(spec.tree(
+                    format=format_string,
+                    color=True,
+                    indent=4,
+                    prefix=(lambda s: gray_hash(s, hlen)) if hashes else None))
+
+        elif mode == 'short':
+            # Print columns of output if not printing flags
+            if not flags:
+
+                def fmt(s):
+                    string = ""
+                    if hashes:
+                        string += gray_hash(s, hlen) + ' '
+                    string += s.format('$-%s$@%s' % (nfmt, vfmt), color=True)
+
+                    return string
+
+                colify(fmt(s) for s in specs)
+            # Print one entry per line if including flags
+            else:
+                for spec in specs:
+                    # Print the hash if necessary
+                    hsh = gray_hash(spec, hlen) + ' ' if hashes else ''
+                    print(hsh + spec.format(format_string, color=True) + '\n')
+
+        else:
+            raise ValueError(
+                "Invalid mode for display_specs: %s. Must be one of (paths,"
+                "deps, short)." % mode)  # NOQA: ignore=E501

lib/spack/spack/cmd/bootstrap.py

@@ -23,7 +23,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-from subprocess import check_call
 
 import llnl.util.tty as tty
 from llnl.util.filesystem import join_path, mkdirp
@@ -31,26 +30,49 @@
 import spack
 from spack.util.executable import which
 
+_SPACK_UPSTREAM = 'https://github.com/llnl/spack'
+
 description = "Create a new installation of spack in another prefix"
 
+
 def setup_parser(subparser):
-    subparser.add_argument('prefix', help="names of prefix where we should install spack")
+    subparser.add_argument(
+        '-r', '--remote', action='store', dest='remote',
+        help="name of the remote to bootstrap from", default='origin')
+    subparser.add_argument(
+        'prefix',
+        help="names of prefix where we should install spack")
 
 
-def get_origin_url():
+def get_origin_info(remote):
     git_dir = join_path(spack.prefix, '.git')
     git = which('git', required=True)
+    try:
+        branch = git('symbolic-ref', '--short', 'HEAD', output=str)
+    except ProcessError:
+        branch = 'develop'
+        tty.warn('No branch found; using default branch: %s' % branch)
+    if remote == 'origin' and \
+       branch not in ('master', 'develop'):
+        branch = 'develop'
+        tty.warn('Unknown branch found; using default branch: %s' % branch)
+    try:
         origin_url = git(
-        '--git-dir=%s' % git_dir, 'config', '--get', 'remote.origin.url',
+            '--git-dir=%s' % git_dir,
+            'config', '--get', 'remote.%s.url' % remote,
             output=str)
-    return origin_url.strip()
+    except ProcessError:
+        origin_url = _SPACK_UPSTREAM
+        tty.warn('No git repository found; '
+                 'using default upstream URL: %s' % origin_url)
+    return (origin_url.strip(), branch.strip())
 
 
 def bootstrap(parser, args):
-    origin_url = get_origin_url()
+    origin_url, branch = get_origin_info(args.remote)
     prefix = args.prefix
 
-    tty.msg("Fetching spack from origin: %s" % origin_url)
+    tty.msg("Fetching spack from '%s': %s" % (args.remote, origin_url))
 
     if os.path.isfile(prefix):
         tty.die("There is already a file at %s" % prefix)
@@ -62,7 +84,8 @@ def bootstrap(parser, args):
 
     files_in_the_way = os.listdir(prefix)
     if files_in_the_way:
-        tty.die("There are already files there!  Delete these files before boostrapping spack.",
+        tty.die("There are already files there! "
+                "Delete these files before boostrapping spack.",
                 *files_in_the_way)
 
     tty.msg("Installing:",
@@ -73,8 +96,10 @@ def bootstrap(parser, args):
     git = which('git', required=True)
     git('init', '--shared', '-q')
     git('remote', 'add', 'origin', origin_url)
-    git('fetch', 'origin', 'master:refs/remotes/origin/master', '-n', '-q')
+    git('fetch', 'origin', '%s:refs/remotes/origin/%s' % (branch, branch),
-    git('reset', '--hard', 'origin/master', '-q')
+                           '-n', '-q')
+    git('reset', '--hard', 'origin/%s' % branch, '-q')
+    git('checkout', '-B', branch, 'origin/%s' % branch, '-q')
 
     tty.msg("Successfully created a new spack in %s" % prefix,
             "Run %s/bin/spack to use this installation." % prefix)

lib/spack/spack/cmd/checksum.py

@@ -42,7 +42,8 @@ def setup_parser(subparser):
         '--keep-stage', action='store_true', dest='keep_stage',
         help="Don't clean up staging area when command completes.")
     subparser.add_argument(
-        'versions', nargs=argparse.REMAINDER, help='Versions to generate checksums for')
+        'versions', nargs=argparse.REMAINDER,
+        help='Versions to generate checksums for')
 
 
 def get_checksums(versions, urls, **kwargs):
@@ -59,10 +60,10 @@ def get_checksums(versions, urls, **kwargs):
             with Stage(url, keep=keep_stage) as stage:
                 stage.fetch()
                 if i == 0 and first_stage_function:
-                    first_stage_function(stage)
+                    first_stage_function(stage, url)
 
-                hashes.append((version,
+                hashes.append((version, spack.util.crypto.checksum(
-                               spack.util.crypto.checksum(hashlib.md5, stage.archive_file)))
+                    hashlib.md5, stage.archive_file)))
                 i += 1
         except FailedDownloadError as e:
             tty.msg("Failed to fetch %s" % url)
@@ -79,12 +80,12 @@ def checksum(parser, args):
     # If the user asked for specific versions, use those.
     if args.versions:
         versions = {}
-        for v in args.versions:
+        for version in args.versions:
-            v = ver(v)
+            version = ver(version)
-            if not isinstance(v, Version):
+            if not isinstance(version, Version):
                 tty.die("Cannot generate checksums for version lists or " +
                         "version ranges.  Use unambiguous versions.")
-            versions[v] = pkg.url_for_version(v)
+            versions[version] = pkg.url_for_version(version)
     else:
         versions = pkg.fetch_remote_versions()
         if not versions:
@@ -111,5 +112,7 @@ def checksum(parser, args):
     if not version_hashes:
         tty.die("Could not fetch any versions for %s" % pkg.name)
 
-    version_lines = ["    version('%s', '%s')" % (v, h) for v, h in version_hashes]
+    version_lines = [
+        "    version('%s', '%s')" % (v, h) for v, h in version_hashes
+    ]
     tty.msg("Checksummed new versions of %s:" % pkg.name, *version_lines)

lib/spack/spack/cmd/common/__init__.py

@@ -0,0 +1,24 @@
+##############################################################################
+# 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
+##############################################################################

lib/spack/spack/cmd/common/arguments.py

@@ -0,0 +1,96 @@
+##############################################################################
+# 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
+##############################################################################
+
+import argparse
+
+import spack.modules
+from spack.util.pattern import Bunch
+__all__ = ['add_common_arguments']
+
+_arguments = {}
+
+
+def add_common_arguments(parser, list_of_arguments):
+    for argument in list_of_arguments:
+        if argument not in _arguments:
+            message = 'Trying to add the non existing argument "{0}" to a command'  # NOQA: ignore=E501
+            raise KeyError(message.format(argument))
+        x = _arguments[argument]
+        parser.add_argument(*x.flags, **x.kwargs)
+
+
+class ConstraintAction(argparse.Action):
+    """Constructs a list of specs based on a constraint given on the command line
+
+    An instance of this class is supposed to be used as an argument action
+    in a parser. It will read a constraint and will attach a list of matching
+    specs to the namespace
+    """
+    qualifiers = {}
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        # Query specs from command line
+        d = self.qualifiers.get(namespace.subparser_name, {})
+        specs = [s for s in spack.installed_db.query(**d)]
+        values = ' '.join(values)
+        if values:
+            specs = [x for x in specs if x.satisfies(values, strict=True)]
+        namespace.specs = specs
+
+parms = Bunch(
+    flags=('constraint',),
+    kwargs={
+        'nargs': '*',
+        'help': 'Constraint to select a subset of installed packages',
+        'action': ConstraintAction
+    })
+_arguments['constraint'] = parms
+
+parms = Bunch(
+    flags=('-m', '--module-type'),
+    kwargs={
+        'help': 'Type of module files',
+        'default': 'tcl',
+        'choices': spack.modules.module_types
+    })
+_arguments['module_type'] = parms
+
+parms = Bunch(
+    flags=('-y', '--yes-to-all'),
+    kwargs={
+        'action': 'store_true',
+        'dest': 'yes_to_all',
+        'help': 'Assume "yes" is the answer to every confirmation asked to the user.'  # NOQA: ignore=E501
+    })
+_arguments['yes_to_all'] = parms
+
+parms = Bunch(
+    flags=('-r', '--dependencies'),
+    kwargs={
+        'action': 'store_true',
+        'dest': 'recurse_dependencies',
+        'help': 'Recursively traverse spec dependencies'
+    })
+_arguments['recurse_dependencies'] = parms

lib/spack/spack/cmd/create.py

@@ -103,54 +103,19 @@ def install(self, spec, prefix):
 ${install}
 """)
 
-
-def make_version_calls(ver_hash_tuples):
-    """Adds a version() call to the package for each version found."""
-    max_len = max(len(str(v)) for v, h in ver_hash_tuples)
-    format = "    version(%%-%ds, '%%s')" % (max_len + 2)
-    return '\n'.join(format % ("'%s'" % v, h) for v, h in ver_hash_tuples)
-
-
-def setup_parser(subparser):
-    subparser.add_argument('url', nargs='?', help="url of package archive")
-    subparser.add_argument(
-        '--keep-stage', action='store_true',
-        help="Don't clean up staging area when command completes.")
-    subparser.add_argument(
-        '-n', '--name', dest='alternate_name', default=None, metavar='NAME',
-        help="Override the autodetected name for the created package.")
-    subparser.add_argument(
-        '-r', '--repo', default=None,
-        help="Path to a repository where the package should be created.")
-    subparser.add_argument(
-        '-N', '--namespace',
-        help="Specify a namespace for the package. Must be the namespace of "
-        "a repository registered with Spack.")
-    subparser.add_argument(
-        '-f', '--force', action='store_true', dest='force',
-        help="Overwrite any existing package file with the same name.")
-
-    setup_parser.subparser = subparser
-
-
-class ConfigureGuesser(object):
-    def __call__(self, stage):
-        """Try to guess the type of build system used by the project.
-        Set any necessary build dependencies or extensions.
-        Set the appropriate default installation instructions."""
-
 # Build dependencies and extensions
-        dependenciesDict = {
+dependencies_dict = {
     'autotools': "# depends_on('foo')",
-            'cmake':     "depends_on('cmake', type='build')",
+    'cmake':     "depends_on('cmake')",
-            'scons':     "depends_on('scons', type='build')",
+    'scons':     "depends_on('scons')",
-            'python':    "extends('python', type=nolink)",
+    'python':    "extends('python')",
     'R':         "extends('R')",
+    'octave':    "extends('octave')",
     'unknown':   "# depends_on('foo')"
 }
 
 # Default installation instructions
-        installDict = {
+install_dict = {
     'autotools': """\
         # FIXME: Modify the configure line to suit your build system here.
         configure('--prefix={0}'.format(prefix))
@@ -182,12 +147,62 @@ def __call__(self, stage):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
           self.stage.source_path)""",
 
+    'octave': """\
+        # FIXME: Add logic to build and install here.
+        octave('--quiet', '--norc',
+               '--built-in-docstrings-file=/dev/null',
+               '--texi-macros-file=/dev/null',
+               '--eval', 'pkg prefix {0}; pkg install {1}'.format(
+                   prefix, self.stage.archive_file))""",
+
     'unknown': """\
         # FIXME: Unknown build system
         make()
         make('install')"""
 }
 
+
+def make_version_calls(ver_hash_tuples):
+    """Adds a version() call to the package for each version found."""
+    max_len = max(len(str(v)) for v, h in ver_hash_tuples)
+    format = "    version(%%-%ds, '%%s')" % (max_len + 2)
+    return '\n'.join(format % ("'%s'" % v, h) for v, h in ver_hash_tuples)
+
+
+def setup_parser(subparser):
+    subparser.add_argument('url', nargs='?', help="url of package archive")
+    subparser.add_argument(
+        '--keep-stage', action='store_true',
+        help="Don't clean up staging area when command completes.")
+    subparser.add_argument(
+        '-n', '--name', dest='alternate_name', default=None, metavar='NAME',
+        help="Override the autodetected name for the created package.")
+    subparser.add_argument(
+        '-r', '--repo', default=None,
+        help="Path to a repository where the package should be created.")
+    subparser.add_argument(
+        '-N', '--namespace',
+        help="Specify a namespace for the package. Must be the namespace of "
+        "a repository registered with Spack.")
+    subparser.add_argument(
+        '-f', '--force', action='store_true', dest='force',
+        help="Overwrite any existing package file with the same name.")
+
+    setup_parser.subparser = subparser
+
+
+class BuildSystemGuesser(object):
+    def __call__(self, stage, url):
+        """Try to guess the type of build system used by a project based on
+        the contents of its archive or the URL it was downloaded from."""
+
+        # Most octave extensions are hosted on Octave-Forge:
+        #     http://octave.sourceforge.net/index.html
+        # They all have the same base URL.
+        if 'downloads.sourceforge.net/octave/' in url:
+            self.build_system = 'octave'
+            return
+
         # 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.
@@ -224,12 +239,6 @@ def __call__(self, stage):
 
         self.build_system = build_system
 
-        # Set any necessary build dependencies or extensions.
-        self.dependencies = dependenciesDict[build_system]
-
-        # Set the appropriate default installation instructions
-        self.install = installDict[build_system]
-
 
 def guess_name_and_version(url, args):
     # Try to deduce name and version of the new package from the URL
@@ -334,8 +343,8 @@ def create(parser, args):
     # Fetch tarballs (prompting user if necessary)
     versions, urls = fetch_tarballs(url, name, version)
 
-    # Try to guess what configure system is used.
+    # Try to guess what build system is used.
-    guesser = ConfigureGuesser()
+    guesser = BuildSystemGuesser()
     ver_hash_tuples = spack.cmd.checksum.get_checksums(
         versions, urls,
         first_stage_function=guesser,
@@ -344,13 +353,13 @@ def create(parser, args):
     if not ver_hash_tuples:
         tty.die("Could not fetch any tarballs for %s" % name)
 
-    # Prepend 'py-' to python package names, by convention.
+    # Add prefix to package name if it is an extension.
     if guesser.build_system == 'python':
-        name = 'py-%s' % name
+        name = 'py-{0}'.format(name)
-
-    # Prepend 'r-' to R package names, by convention.
     if guesser.build_system == 'R':
-        name = 'r-%s' % name
+        name = 'r-{0}'.format(name)
+    if guesser.build_system == 'octave':
+        name = 'octave-{0}'.format(name)
 
     # Create a directory for the new package.
     pkg_path = repo.filename_for_package_name(name)
@@ -367,8 +376,8 @@ def create(parser, args):
                 class_name=mod_to_class(name),
                 url=url,
                 versions=make_version_calls(ver_hash_tuples),
-                dependencies=guesser.dependencies,
+                dependencies=dependencies_dict[guesser.build_system],
-                install=guesser.install))
+                install=install_dict[guesser.build_system]))
 
     # If everything checks out, go ahead and edit.
     spack.editor(pkg_path)

lib/spack/spack/cmd/find.py

@@ -31,7 +31,7 @@
 from llnl.util.lang import *
 from llnl.util.tty.colify import *
 from llnl.util.tty.color import *
-from llnl.util.lang import *
+from spack.cmd import display_specs
 
 description = "Find installed spack packages"
 
@@ -104,89 +104,6 @@ def setup_parser(subparser):
                            help='optional specs to filter results')
 
 
-def gray_hash(spec, length):
-    return colorize('@K{%s}' % spec.dag_hash(length))
-
-
-def display_specs(specs, **kwargs):
-    mode = kwargs.get('mode', 'short')
-    hashes = kwargs.get('long', False)
-    namespace = kwargs.get('namespace', False)
-    flags = kwargs.get('show_flags', False)
-    variants = kwargs.get('variants', False)
-
-    hlen = 7
-    if kwargs.get('very_long', False):
-        hashes = True
-        hlen = None
-
-    nfmt = '.' if namespace else '_'
-    ffmt = '$%+' if flags else ''
-    vfmt = '$+' if variants else ''
-    format_string = '$%s$@%s%s' % (nfmt, ffmt, vfmt)
-
-    # Make a dict with specs keyed by architecture and compiler.
-    index = index_by(specs, ('architecture', 'compiler'))
-
-    # Traverse the index and print out each package
-    for i, (architecture, compiler) in enumerate(sorted(index)):
-        if i > 0:
-            print
-
-        header = "%s{%s} / %s{%s}" % (spack.spec.architecture_color,
-                                      architecture, spack.spec.compiler_color,
-                                      compiler)
-        tty.hline(colorize(header), char='-')
-
-        specs = index[(architecture, compiler)]
-        specs.sort()
-
-        abbreviated = [s.format(format_string, color=True) for s in specs]
-        if mode == 'paths':
-            # Print one spec per line along with prefix path
-            width = max(len(s) for s in abbreviated)
-            width += 2
-            format = "    %%-%ds%%s" % width
-
-            for abbrv, spec in zip(abbreviated, specs):
-                if hashes:
-                    print(gray_hash(spec, hlen), )
-                print(format % (abbrv, spec.prefix))
-
-        elif mode == 'deps':
-            for spec in specs:
-                print(spec.tree(
-                    format=format_string,
-                    color=True,
-                    indent=4,
-                    prefix=(lambda s: gray_hash(s, hlen)) if hashes else None))
-
-        elif mode == 'short':
-            # Print columns of output if not printing flags
-            if not flags:
-
-                def fmt(s):
-                    string = ""
-                    if hashes:
-                        string += gray_hash(s, hlen) + ' '
-                    string += s.format('$-%s$@%s' % (nfmt, vfmt), color=True)
-
-                    return string
-
-                colify(fmt(s) for s in specs)
-            # Print one entry per line if including flags
-            else:
-                for spec in specs:
-                    # Print the hash if necessary
-                    hsh = gray_hash(spec, hlen) + ' ' if hashes else ''
-                    print(hsh + spec.format(format_string, color=True) + '\n')
-
-        else:
-            raise ValueError(
-                "Invalid mode for display_specs: %s. Must be one of (paths,"
-                "deps, short)." % mode)  # NOQA: ignore=E501
-
-
 def query_arguments(args):
     # Check arguments
     if args.explicit and args.implicit:

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/cmd/module.py

@@ -23,135 +23,233 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from __future__ import print_function
+
+import collections
 import os
 import shutil
 import sys
 
 import llnl.util.tty as tty
 import spack.cmd
-from llnl.util.filesystem import mkdirp
+import spack.cmd.common.arguments as arguments
+import llnl.util.filesystem as filesystem
 from spack.modules import module_types
-from spack.util.string import *
 
-description = "Manipulate modules and dotkits."
+description = "Manipulate module files"
+
+# Dictionary that will be populated with the list of sub-commands
+# Each sub-command must be callable and accept 3 arguments :
+# - mtype : the type of the module file
+# - specs : the list of specs to be processed
+# - args : namespace containing the parsed command line arguments
+callbacks = {}
+
+
+def subcommand(subparser_name):
+    """Registers a function in the callbacks dictionary"""
+    def decorator(callback):
+        callbacks[subparser_name] = callback
+        return callback
+    return decorator
 
 
 def setup_parser(subparser):
-    sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='module_command')
+    sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='subparser_name')
 
-    sp.add_parser('refresh', help='Regenerate all module files.')
+    # spack module refresh
+    refresh_parser = sp.add_parser('refresh', help='Regenerate module files')
+    refresh_parser.add_argument(
+        '--delete-tree',
+        help='Delete the module file tree before refresh',
+        action='store_true'
+    )
+    arguments.add_common_arguments(
+        refresh_parser, ['constraint', 'module_type', 'yes_to_all']
+    )
 
-    find_parser = sp.add_parser('find', help='Find module files for packages.')
+    # spack module find
+    find_parser = sp.add_parser('find', help='Find module files for packages')
+    arguments.add_common_arguments(find_parser, ['constraint', 'module_type'])
 
-    find_parser.add_argument(
+    # spack module rm
-        'module_type',
+    rm_parser = sp.add_parser('rm', help='Remove module files')
-        help="Type of module to find file for. [" +
+    arguments.add_common_arguments(
-        '|'.join(module_types) + "]")
+        rm_parser, ['constraint', 'module_type', 'yes_to_all']
+    )
 
-    find_parser.add_argument(
+    # spack module loads
-        '-r', '--dependencies', action='store_true',
+    loads_parser = sp.add_parser(
-        dest='recurse_dependencies',
+        'loads',
-        help='Recursively traverse dependencies for modules to load.')
+        help='Prompt the list of modules associated with a constraint'
-
+    )
-    find_parser.add_argument(
+    loads_parser.add_argument(
-        '-s', '--shell', action='store_true', dest='shell',
+        '--input-only', action='store_false', dest='shell',
-        help='Generate shell script (instead of input for module command)')
+        help='Generate input for module command (instead of a shell script)'
-
+    )
-    find_parser.add_argument(
+    loads_parser.add_argument(
-        '-p', '--prefix', dest='prefix',
+        '-p', '--prefix', dest='prefix', default='',
-        help='Prepend to module names when issuing module load commands')
+        help='Prepend to module names when issuing module load commands'
-
+    )
-    find_parser.add_argument(
+    arguments.add_common_arguments(
-        'spec', nargs='+',
+        loads_parser, ['constraint', 'module_type', 'recurse_dependencies']
-        help='spec to find a module file for.')
+    )
 
 
-def module_find(mtype, flags, spec_array):
+class MultipleMatches(Exception):
-    """Look at all installed packages and see if the spec provided
+    pass
+
+
+class NoMatch(Exception):
+    pass
+
+
+@subcommand('loads')
+def loads(mtype, specs, args):
+    """Prompt the list of modules associated with a list of specs"""
+    # Get a comprehensive list of specs
+    if args.recurse_dependencies:
+        specs_from_user_constraint = specs[:]
+        specs = []
+        # FIXME : during module file creation nodes seem to be visited
+        # FIXME : multiple times even if cover='nodes' is given. This
+        # FIXME : work around permits to get a unique list of spec anyhow.
+        # FIXME : (same problem as in spack/modules.py)
+        seen = set()
+        seen_add = seen.add
+        for spec in specs_from_user_constraint:
+            specs.extend(
+                [item for item in spec.traverse(order='post', cover='nodes') if not (item in seen or seen_add(item))]  # NOQA: ignore=E501
+            )
+
+    module_cls = module_types[mtype]
+    modules = [(spec, module_cls(spec).use_name)
+               for spec in specs if os.path.exists(module_cls(spec).file_name)]
+
+    module_commands = {
+        'tcl': 'module load ',
+        'dotkit': 'dotkit use '
+    }
+
+    d = {
+        'command': '' if not args.shell else module_commands[mtype],
+        'prefix': args.prefix
+    }
+
+    prompt_template = '{comment}{command}{prefix}{name}'
+    for spec, mod in modules:
+        d['comment'] = '' if not args.shell else '# {0}\n'.format(
+            spec.format())
+        d['name'] = mod
+        print(prompt_template.format(**d))
+
+
+@subcommand('find')
+def find(mtype, specs, args):
+    """
+    Look at all installed packages and see if the spec provided
     matches any.  If it does, check whether there is a module file
     of type <mtype> there, and print out the name that the user
     should type to use that package's module.
-    prefix:
-        Prepend this to module names when issuing "module load" commands.
-        Some systems seem to need it.
     """
-    if mtype not in module_types:
+    if len(specs) == 0:
-        tty.die("Invalid module type: '%s'.  Options are %s" %
+        raise NoMatch()
-                (mtype, comma_or(module_types)))
 
-    # --------------------------------------
+    if len(specs) > 1:
-    def _find_modules(spec, modules_list):
+        raise MultipleMatches()
-        """Finds all modules and sub-modules for a spec"""
-        if str(spec.version) == 'system':
-            # No Spack module for system-installed packages
-            return
-
-        if flags.recurse_dependencies:
-            for dep in spec.dependencies():
-                _find_modules(dep, modules_list)
 
+    spec = specs.pop()
     mod = module_types[mtype](spec)
     if not os.path.isfile(mod.file_name):
         tty.die("No %s module is installed for %s" % (mtype, spec))
-        modules_list.append((spec, mod))
-
-
-    # --------------------------------------
-    raw_specs = spack.cmd.parse_specs(spec_array)
-    modules = set()    # Modules we will load
-    seen = set()
-    for raw_spec in raw_specs:
-
-        # ----------- Make sure the spec only resolves to ONE thing
-        specs = spack.installed_db.query(raw_spec)
-        if len(specs) == 0:
-            tty.die("No installed packages match spec %s" % raw_spec)
-
-        if len(specs) > 1:
-            tty.error("Multiple matches for spec %s.  Choose one:" % raw_spec)
-            for s in specs:
-                sys.stderr.write(s.tree(color=True))
-            sys.exit(1)
-        spec = specs[0]
-
-        # ----------- Chase down modules for it and all its dependencies
-        modules_dups = list()
-        _find_modules(spec, modules_dups)
-
-        # Remove duplicates while keeping order
-        modules_unique = list()
-        for spec,mod in modules_dups:
-            if mod.use_name not in seen:
-                modules_unique.append((spec,mod))
-                seen.add(mod.use_name)
-
-        # Output...
-        if flags.shell:
-            module_cmd = {'tcl': 'module load', 'dotkit': 'dotkit use'}[mtype]
-        for spec,mod in modules_unique:
-            if flags.shell:
-                print('# %s' % spec.format())
-                print('%s %s%s' % (module_cmd, flags.prefix, mod.use_name))
-            else:
     print(mod.use_name)
 
-def module_refresh():
-    """Regenerate all module files for installed packages known to
-       spack (some packages may no longer exist)."""
-    specs = [s for s in spack.installed_db.query(installed=True, known=True)]
 
-    for name, cls in module_types.items():
+@subcommand('rm')
-        tty.msg("Regenerating %s module files." % name)
+def rm(mtype, specs, args):
-        if os.path.isdir(cls.path):
+    """Deletes module files associated with items in specs"""
+    module_cls = module_types[mtype]
+    specs_with_modules = [
+        spec for spec in specs if os.path.exists(module_cls(spec).file_name)]
+    modules = [module_cls(spec) for spec in specs_with_modules]
+
+    if not modules:
+        tty.msg('No module file matches your query')
+        raise SystemExit(1)
+
+    # Ask for confirmation
+    if not args.yes_to_all:
+        tty.msg('You are about to remove {0} module files the following specs:\n'.format(mtype))  # NOQA: ignore=E501
+        spack.cmd.display_specs(specs_with_modules, long=True)
+        print('')
+        spack.cmd.ask_for_confirmation('Do you want to proceed ? ')
+
+    # Remove the module files
+    for s in modules:
+        s.remove()
+
+
+@subcommand('refresh')
+def refresh(mtype, specs, args):
+    """Regenerate module files for item in specs"""
+    # Prompt a message to the user about what is going to change
+    if not specs:
+        tty.msg('No package matches your query')
+        return
+
+    if not args.yes_to_all:
+        tty.msg('You are about to regenerate {name} module files for the following specs:\n'.format(name=mtype))  # NOQA: ignore=E501
+        spack.cmd.display_specs(specs, long=True)
+        print('')
+        spack.cmd.ask_for_confirmation('Do you want to proceed ? ')
+
+    cls = module_types[mtype]
+
+    # Detect name clashes
+    writers = [cls(spec) for spec in specs]
+    file2writer = collections.defaultdict(list)
+    for item in writers:
+        file2writer[item.file_name].append(item)
+
+    if len(file2writer) != len(writers):
+        message = 'Name clashes detected in module files:\n'
+        for filename, writer_list in file2writer.items():
+            if len(writer_list) > 1:
+                message += '\nfile : {0}\n'.format(filename)
+                for x in writer_list:
+                    message += 'spec : {0}\n'.format(x.spec.format(color=True))
+        tty.error(message)
+        tty.error('Operation aborted')
+        raise SystemExit(1)
+
+    # Proceed regenerating module files
+    tty.msg('Regenerating {name} module files'.format(name=mtype))
+    if os.path.isdir(cls.path) and args.delete_tree:
         shutil.rmtree(cls.path, ignore_errors=False)
-        mkdirp(cls.path)
+    filesystem.mkdirp(cls.path)
-        for spec in specs:
+    for x in writers:
-            cls(spec).write()
+        x.write(overwrite=True)
 
 
 def module(parser, args):
-    if args.module_command == 'refresh':
+    # Qualifiers to be used when querying the db for specs
-        module_refresh()
+    constraint_qualifiers = {
+        'refresh': {
+            'installed': True,
+            'known': True
+        },
+    }
+    arguments.ConstraintAction.qualifiers.update(constraint_qualifiers)
 
-    elif args.module_command == 'find':
+    module_type = args.module_type
-        module_find(args.module_type, args, args.spec)
+    constraint = args.constraint
+    try:
+        callbacks[args.subparser_name](module_type, args.specs, args)
+    except MultipleMatches:
+        message = 'the constraint \'{query}\' matches multiple packages, and this is not allowed in this context'  # NOQA: ignore=E501
+        tty.error(message.format(query=constraint))
+        for s in args.specs:
+            sys.stderr.write(s.format(color=True) + '\n')
+        raise SystemExit(1)
+    except NoMatch:
+        message = 'the constraint \'{query}\' match no package, and this is not allowed in this context'  # NOQA: ignore=E501
+        tty.die(message.format(query=constraint))

lib/spack/spack/cmd/package-list.py

@@ -22,10 +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 re
 import cgi
 from StringIO import StringIO
-import llnl.util.tty as tty
 from llnl.util.tty.colify import *
 import spack
 
@@ -34,8 +32,8 @@
 
 def github_url(pkg):
     """Link to a package file on github."""
-    return ("https://github.com/llnl/spack/blob/master/var/spack/packages/%s/package.py" %
+    url = "https://github.com/llnl/spack/blob/master/var/spack/packages/%s/package.py"  # NOQA: ignore=E501
-            pkg.name)
+    return (url % pkg.name)
 
 
 def rst_table(elts):
@@ -49,6 +47,7 @@ def rst_table(elts):
 def print_rst_package_list():
     """Print out information on all packages in restructured text."""
     pkgs = sorted(spack.repo.all_packages(), key=lambda s: s.name.lower())
+    pkg_names = [p.name for p in pkgs]
 
     print ".. _package-list:"
     print
@@ -62,7 +61,7 @@ def print_rst_package_list():
 
     print "Spack currently has %d mainline packages:" % len(pkgs)
     print
-    print rst_table("`%s`_" % p.name for p in pkgs)
+    print rst_table("`%s`_" % p for p in pkg_names)
     print
     print "-----"
 
@@ -79,14 +78,15 @@ def print_rst_package_list():
         print
         if pkg.versions:
             print "Versions:"
-            print "  " + ", ".join(str(v) for v in reversed(sorted(pkg.versions)))
+            print "  " + ", ".join(str(v) for v in
+                                   reversed(sorted(pkg.versions)))
 
-        for deptype in ('build', 'link', 'run'):
+        for deptype in spack.alldeps:
-            deps = pkg.dependencies(deptype)
+            deps = pkg.dependencies_of_type(deptype)
             if deps:
                 print "%s Dependencies" % deptype.capitalize()
-                print "  " + ", ".join("`%s`_" % d if d != "mpi" else d
+                print "  " + ", ".join("%s_" % d if d in pkg_names
-                                       for d in build_deps)
+                                       else d for d in deps)
                 print
 
         print "Description:"

lib/spack/spack/cmd/uninstall.py

@@ -30,7 +30,6 @@
 import spack
 import spack.cmd
 import spack.repository
-from spack.cmd.find import display_specs
 
 description = "Remove an installed package"
 
@@ -47,17 +46,6 @@
 }
 
 
-def ask_for_confirmation(message):
-    while True:
-        tty.msg(message + '[y/n]')
-        choice = raw_input().lower()
-        if choice == 'y':
-            break
-        elif choice == 'n':
-            raise SystemExit('Operation aborted')
-        tty.warn('Please reply either "y" or "n"')
-
-
 def setup_parser(subparser):
     subparser.add_argument(
         '-f', '--force', action='store_true', dest='force',
@@ -65,32 +53,37 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-a', '--all', action='store_true', dest='all',
         help="USE CAREFULLY. Remove ALL installed packages that match each " +
-             "supplied spec. i.e., if you say uninstall libelf, ALL versions of " +
+             "supplied spec. i.e., if you say uninstall libelf, ALL versions of " +  # NOQA: ignore=E501
-             "libelf are uninstalled. This is both useful and dangerous, like rm -r.")
+             "libelf are uninstalled. This is both useful and dangerous, like rm -r.")  # NOQA: ignore=E501
     subparser.add_argument(
         '-d', '--dependents', action='store_true', dest='dependents',
-        help='Also uninstall any packages that depend on the ones given via command line.'
+        help='Also uninstall any packages that depend on the ones given via command line.'  # NOQA: ignore=E501
     )
     subparser.add_argument(
         '-y', '--yes-to-all', action='store_true', dest='yes_to_all',
-        help='Assume "yes" is the answer to every confirmation asked to the user.'
+        help='Assume "yes" is the answer to every confirmation asked to the user.'  # NOQA: ignore=E501
 
     )
-    subparser.add_argument('packages', nargs=argparse.REMAINDER, help="specs of packages to uninstall")
+    subparser.add_argument(
+        'packages',
+        nargs=argparse.REMAINDER,
+        help="specs of packages to uninstall"
+    )
 
 
 def concretize_specs(specs, allow_multiple_matches=False, force=False):
-    """
+    """Returns a list of specs matching the non necessarily
-    Returns a list of specs matching the non necessarily concretized specs given from cli
+    concretized specs given from cli
 
     Args:
         specs: list of specs to be matched against installed packages
-        allow_multiple_matches : boolean (if True multiple matches for each item in specs are admitted)
+        allow_multiple_matches : if True multiple matches are admitted
 
     Return:
         list of specs
     """
-    specs_from_cli = []  # List of specs that match expressions given via command line
+    # List of specs that match expressions given via command line
+    specs_from_cli = []
     has_errors = False
     for spec in specs:
         matching = spack.installed_db.query(spec)
@@ -99,7 +92,7 @@ def concretize_specs(specs, allow_multiple_matches=False, force=False):
         if not allow_multiple_matches and len(matching) > 1:
             tty.error("%s matches multiple packages:" % spec)
             print()
-            display_specs(matching, **display_args)
+            spack.cmd.display_specs(matching, **display_args)
             print()
             has_errors = True
 
@@ -116,8 +109,8 @@ def concretize_specs(specs, allow_multiple_matches=False, force=False):
 
 
 def installed_dependents(specs):
-    """
+    """Returns a dictionary that maps a spec with a list of its
-    Returns a dictionary that maps a spec with a list of its installed dependents
+    installed dependents
 
     Args:
         specs: list of specs to be checked for dependents
@@ -147,7 +140,7 @@ def do_uninstall(specs, force):
         try:
             # should work if package is known to spack
             packages.append(item.package)
-        except spack.repository.UnknownPackageError as e:
+        except spack.repository.UnknownPackageError:
             # The package.py file has gone away -- but still
             # want to uninstall.
             spack.Package(item).do_uninstall(force=True)
@@ -169,17 +162,20 @@ def uninstall(parser, args):
     with spack.installed_db.write_transaction():
         specs = spack.cmd.parse_specs(args.packages)
         # Gets the list of installed specs that match the ones give via cli
-        uninstall_list = concretize_specs(specs, args.all, args.force)  # takes care of '-a' is given in the cli
+        # takes care of '-a' is given in the cli
-        dependent_list = installed_dependents(uninstall_list)  # takes care of '-d'
+        uninstall_list = concretize_specs(specs, args.all, args.force)
+        dependent_list = installed_dependents(
+            uninstall_list)  # takes care of '-d'
 
         # Process dependent_list and update uninstall_list
         has_error = False
         if dependent_list and not args.dependents and not args.force:
             for spec, lst in dependent_list.items():
-                tty.error("Will not uninstall %s" % spec.format("$_$@$%@$#", color=True))
+                tty.error("Will not uninstall %s" %
+                          spec.format("$_$@$%@$#", color=True))
                 print('')
                 print("The following packages depend on it:")
-                display_specs(lst, **display_args)
+                spack.cmd.display_specs(lst, **display_args)
                 print('')
                 has_error = True
         elif args.dependents:
@@ -188,14 +184,14 @@ def uninstall(parser, args):
             uninstall_list = list(set(uninstall_list))
 
         if has_error:
-            tty.die('You can use spack uninstall --dependents to uninstall these dependencies as well')
+            tty.die('You can use spack uninstall --dependents to uninstall these dependencies as well')  # NOQA: ignore=E501
 
         if not args.yes_to_all:
             tty.msg("The following packages will be uninstalled : ")
             print('')
-            display_specs(uninstall_list, **display_args)
+            spack.cmd.display_specs(uninstall_list, **display_args)
             print('')
-            ask_for_confirmation('Do you want to proceed ? ')
+            spack.cmd.ask_for_confirmation('Do you want to proceed ? ')
 
         # Uninstall everything on the list
         do_uninstall(uninstall_list, args.force)

lib/spack/spack/config.py

@@ -328,6 +328,11 @@
                 'anyOf': [
                     {
                         'properties': {
+                            'hash_length': {
+                                'type': 'integer',
+                                'minimum': 0,
+                                'default': 7
+                            },
                             'whitelist': {'$ref': '#/definitions/array_of_strings'},
                             'blacklist': {'$ref': '#/definitions/array_of_strings'},
                             'naming_scheme': {
@@ -492,8 +497,15 @@ def clear(self):
         """Empty cached config information."""
         self.sections = {}
 
+"""Default configuration scope is the lowest-level scope. These are
+   versioned with Spack and can be overridden by sites or users."""
+ConfigScope('defaults', os.path.join(spack.etc_path, 'spack', 'defaults'))
 
-ConfigScope('site', os.path.join(spack.etc_path, 'spack')),
+"""Site configuration is per spack instance, for sites or projects.
+   No site-level configs should be checked into spack by default."""
+ConfigScope('site', os.path.join(spack.etc_path, 'spack'))
+
+"""User configuration can override both spack defaults and site config."""
 ConfigScope('user', os.path.expanduser('~/.spack'))
 
 

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/modules.py

@@ -188,6 +188,8 @@ def parse_config_options(module_generator):
     #####
 
     # Automatic loading loads
+    module_file_actions['hash_length'] = module_configuration.get(
+        'hash_length', 7)
     module_file_actions['autoload'] = dependencies(
         module_generator.spec, module_file_actions.get('autoload', 'none'))
     # Prerequisites
@@ -237,6 +239,7 @@ class EnvModule(object):
     formats = {}
 
     class __metaclass__(type):
+
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
             if cls.name != 'env_module' and cls.name in CONFIGURATION[
@@ -295,7 +298,9 @@ def use_name(self):
             if constraint in self.spec:
                 suffixes.append(suffix)
         # Always append the hash to make the module file unique
-        suffixes.append(self.spec.dag_hash())
+        hash_length = configuration.pop('hash_length', 7)
+        if hash_length != 0:
+            suffixes.append(self.spec.dag_hash(length=hash_length))
         name = '-'.join(suffixes)
         return name
 
@@ -338,7 +343,7 @@ def blacklisted(self):
 
         return False
 
-    def write(self):
+    def write(self, overwrite=False):
         """
         Writes out a module file for this object.
 
@@ -399,6 +404,15 @@ def write(self):
         for line in self.module_specific_content(module_configuration):
             module_file_content += line
 
+        # Print a warning in case I am accidentally overwriting
+        # a module file that is already there (name clash)
+        if not overwrite and os.path.exists(self.file_name):
+            message = 'Module file already exists : skipping creation\n'
+            message += 'file : {0.file_name}\n'
+            message += 'spec : {0.spec}'
+            tty.warn(message.format(self))
+            return
+
         # Dump to file
         with open(self.file_name, 'w') as f:
             f.write(module_file_content)
@@ -454,7 +468,7 @@ def remove(self):
 
 class Dotkit(EnvModule):
     name = 'dotkit'
-
+    path = join_path(spack.share_path, 'dotkit')
     environment_modifications_formats = {
         PrependPath: 'dk_alter {name} {value}\n',
         SetEnv: 'dk_setenv {name} {value}\n'
@@ -466,7 +480,7 @@ class Dotkit(EnvModule):
 
     @property
     def file_name(self):
-        return join_path(spack.share_path, "dotkit", self.spec.architecture,
+        return join_path(self.path, self.spec.architecture,
                          '%s.dk' % self.use_name)
 
     @property
@@ -494,7 +508,7 @@ def prerequisite(self, spec):
 
 class TclModule(EnvModule):
     name = 'tcl'
-
+    path = join_path(spack.share_path, "modules")
     environment_modifications_formats = {
         PrependPath: 'prepend-path --delim "{delim}" {name} \"{value}\"\n',
         AppendPath: 'append-path   --delim "{delim}" {name} \"{value}\"\n',
@@ -514,7 +528,7 @@ class TclModule(EnvModule):
 
     @property
     def file_name(self):
-        return join_path(spack.share_path, "modules", self.spec.architecture, self.use_name)
+        return join_path(self.path, self.spec.architecture, self.use_name)
 
     @property
     def header(self):

lib/spack/spack/package.py

@@ -64,7 +64,7 @@
 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
+from spack.util.executable import ProcessError, which
 from spack.version import *
 
 """Allowed URL schemes for spack packages."""
@@ -718,6 +718,11 @@ 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):
         """
@@ -1063,7 +1068,8 @@ def do_install(self,
         run_tests   -- Run 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:
@@ -1713,6 +1719,13 @@ def install_dependency_symlinks(pkg, spec, prefix):
     flatten_dependencies(spec, prefix)
 
 
+def use_cray_compiler_names():
+    """Compiler names for builds that rely on cray compiler names."""
+    os.environ['CC'] = 'cc'
+    os.environ['CXX'] = 'CC'
+    os.environ['FC'] = 'ftn'
+    os.environ['F77'] = 'ftn'
+
 def flatten_dependencies(spec, flat_dir):
     """Make each dependency of spec present in dir via symlink."""
     for dep in spec.traverse(root=False):

lib/spack/spack/platforms/cray_xc.py

@@ -2,6 +2,8 @@
 from spack.architecture import Platform, Target
 from spack.operating_systems.linux_distro import LinuxDistro
 from spack.operating_systems.cnl import Cnl
+from spack.util.executable import which
+
 
 class CrayXc(Platform):
     priority    = 20
@@ -9,7 +11,6 @@ class CrayXc(Platform):
     back_end    = 'ivybridge'
     default     = 'ivybridge'
 
-    front_os    = "SuSE11"
     back_os     = "CNL10"
     default_os  = "CNL10"
 
@@ -37,10 +38,22 @@ def __init__(self):
         self.add_target('haswell',
                         Target('haswell', 'craype-haswell'))
 
-        self.add_operating_system('SuSE11', LinuxDistro())
+        # Front end of the cray platform is a linux distro.
+        linux_dist = LinuxDistro()
+        self.front_os = str(linux_dist)
+        self.add_operating_system(str(linux_dist), linux_dist)
         self.add_operating_system('CNL10', Cnl())
 
     @classmethod
     def detect(self):
-        return os.path.exists('/opt/cray/craype')
+        try:
-
+            cc_verbose = which('ftn')
+            text = cc_verbose('-craype-verbose',
+                              output=str, error=str,
+                              ignore_errors=True).split()
+            if '-D__CRAYXC' in text:
+                return True
+            else:
+                return False
+        except:
+            return False

lib/spack/spack/preferred_packages.py

@@ -26,8 +26,10 @@
 import spack
 from spack.version import *
 
+
 class PreferredPackages(object):
-    _default_order = {'compiler' : [ 'gcc', 'intel', 'clang', 'pgi', 'xlc' ] } # Arbitrary, but consistent
+    # Arbitrary, but consistent
+    _default_order = {'compiler': ['gcc', 'intel', 'clang', 'pgi', 'xlc']}
 
     def __init__(self):
         self.preferred = spack.config.get_config('packages')
@@ -35,24 +37,25 @@ def __init__(self):
 
     # Given a package name, sort component (e.g, version, compiler, ...), and
     # a second_key (used by providers), return the list
-    def _order_for_package(self, pkgname, component, second_key, test_all=True):
+    def _order_for_package(self, pkgname, component, second_key,
+                           test_all=True):
         pkglist = [pkgname]
         if test_all:
             pkglist.append('all')
         for pkg in pkglist:
             order = self.preferred.get(pkg, {}).get(component, {})
-            if type(order) is dict:
+            if isinstance(order, dict) and second_key:
                 order = order.get(second_key, {})
             if not order:
                 continue
             return [str(s).strip() for s in order]
         return []
 
-
     # A generic sorting function. Given a package name and sort
     # component, return less-than-0, 0, or greater-than-0 if
     # a is respectively less-than, equal to, or greater than b.
-    def _component_compare(self, pkgname, component, a, b, reverse_natural_compare, second_key):
+    def _component_compare(self, pkgname, component, a, b,
+                           reverse_natural_compare, second_key):
         if a is None:
             return -1
         if b is None:
@@ -84,92 +87,102 @@ def _component_compare(self, pkgname, component, a, b, reverse_natural_compare,
         else:
             return 0
 
-
     # A sorting function for specs.  Similar to component_compare, but
     # a and b are considered to match entries in the sorting list if they
     # satisfy the list component.
-    def _spec_compare(self, pkgname, component, a, b, reverse_natural_compare, second_key):
+    def _spec_compare(self, pkgname, component, a, b,
-        if not a or not a.concrete:
+                      reverse_natural_compare, second_key):
+        if not a or (not a.concrete and not second_key):
             return -1
-        if not b or not b.concrete:
+        if not b or (not b.concrete and not second_key):
             return 1
         specs = self._spec_for_pkgname(pkgname, component, second_key)
         a_index = None
         b_index = None
         reverse = -1 if reverse_natural_compare else 1
         for i, cspec in enumerate(specs):
-            if a_index == None and (cspec.satisfies(a) or a.satisfies(cspec)):
+            if a_index is None and (cspec.satisfies(a) or a.satisfies(cspec)):
                 a_index = i
                 if b_index:
                     break
-            if b_index == None and (cspec.satisfies(b) or b.satisfies(cspec)):
+            if b_index is None and (cspec.satisfies(b) or b.satisfies(cspec)):
                 b_index = i
                 if a_index:
                     break
 
-        if   a_index != None and b_index == None: return -1
+        if a_index is not None and b_index is None:
-        elif a_index == None and b_index != None: return 1
+            return -1
-        elif a_index != None and b_index == a_index: return -1 * cmp(a, b)
+        elif a_index is None and b_index is not None:
-        elif a_index != None and b_index != None and a_index != b_index: return cmp(a_index, b_index)
+            return 1
-        else: return cmp(a, b) * reverse
+        elif a_index is not None and b_index == a_index:
-
+            return -1 * cmp(a, b)
-
+        elif (a_index is not None and b_index is not None and
+              a_index != b_index):
+            return cmp(a_index, b_index)
+        else:
+            return cmp(a, b) * reverse
 
     # Given a sort order specified by the pkgname/component/second_key, return
     # a list of CompilerSpecs, VersionLists, or Specs for that sorting list.
     def _spec_for_pkgname(self, pkgname, component, second_key):
         key = (pkgname, component, second_key)
-        if not key in self._spec_for_pkgname_cache:
+        if key not in self._spec_for_pkgname_cache:
             pkglist = self._order_for_package(pkgname, component, second_key)
             if not pkglist:
                 if component in self._default_order:
                     pkglist = self._default_order[component]
             if component == 'compiler':
-                self._spec_for_pkgname_cache[key] = [spack.spec.CompilerSpec(s) for s in pkglist]
+                self._spec_for_pkgname_cache[key] = \
+                    [spack.spec.CompilerSpec(s) for s in pkglist]
             elif component == 'version':
-                self._spec_for_pkgname_cache[key] = [VersionList(s) for s in pkglist]
+                self._spec_for_pkgname_cache[key] = \
+                    [VersionList(s) for s in pkglist]
             else:
-                self._spec_for_pkgname_cache[key] = [spack.spec.Spec(s) for s in pkglist]
+                self._spec_for_pkgname_cache[key] = \
+                    [spack.spec.Spec(s) for s in pkglist]
         return self._spec_for_pkgname_cache[key]
 
-
     def provider_compare(self, pkgname, provider_str, a, b):
-        """Return less-than-0, 0, or greater than 0 if a is respecively less-than, equal-to, or
+        """Return less-than-0, 0, or greater than 0 if a is respecively
-           greater-than b. A and b are possible implementations of provider_str.
+           less-than, equal-to, or greater-than b. A and b are possible
-           One provider is less-than another if it is preferred over the other.
+           implementations of provider_str. One provider is less-than another
-           For example, provider_compare('scorep', 'mpi', 'mvapich', 'openmpi') would return -1 if
+           if it is preferred over the other. For example,
-           mvapich should be preferred over openmpi for scorep."""
+           provider_compare('scorep', 'mpi', 'mvapich', 'openmpi') would
-        return self._spec_compare(pkgname, 'providers', a, b, False, provider_str)
+           return -1 if mvapich should be preferred over openmpi for scorep."""
-
+        return self._spec_compare(pkgname, 'providers', a, b, False,
+                                  provider_str)
 
     def spec_has_preferred_provider(self, pkgname, provider_str):
-        """Return True iff the named package has a list of preferred provider"""
+        """Return True iff the named package has a list of preferred
-        return bool(self._order_for_package(pkgname, 'providers', provider_str, False))
+           providers"""
-
+        return bool(self._order_for_package(pkgname, 'providers',
+                    provider_str, False))
 
     def version_compare(self, pkgname, a, b):
         """Return less-than-0, 0, or greater than 0 if version a of pkgname is
-           respecively less-than, equal-to, or greater-than version b of pkgname.
+           respectively less-than, equal-to, or greater-than version b of
-           One version is less-than another if it is preferred over the other."""
+           pkgname. One version is less-than another if it is preferred over
+           the other."""
         return self._spec_compare(pkgname, 'version', a, b, True, None)
 
-
     def variant_compare(self, pkgname, a, b):
         """Return less-than-0, 0, or greater than 0 if variant a of pkgname is
-           respecively less-than, equal-to, or greater-than variant b of pkgname.
+           respectively less-than, equal-to, or greater-than variant b of
-           One variant is less-than another if it is preferred over the other."""
+           pkgname. One variant is less-than another if it is preferred over
+           the other."""
         return self._component_compare(pkgname, 'variant', a, b, False, None)
 
-
     def architecture_compare(self, pkgname, a, b):
-        """Return less-than-0, 0, or greater than 0 if architecture a of pkgname is
+        """Return less-than-0, 0, or greater than 0 if architecture a of pkgname
-           respecively less-than, equal-to, or greater-than architecture b of pkgname.
+           is respectively less-than, equal-to, or greater-than architecture b
-           One architecture is less-than another if it is preferred over the other."""
+           of pkgname. One architecture is less-than another if it is preferred
-        return self._component_compare(pkgname, 'architecture', a, b, False, None)
+           over the other."""
-
+        return self._component_compare(pkgname, 'architecture', a, b,
+                                       False, None)
 
     def compiler_compare(self, pkgname, a, b):
         """Return less-than-0, 0, or greater than 0 if compiler a of pkgname is
-           respecively less-than, equal-to, or greater-than compiler b of pkgname.
+           respecively less-than, equal-to, or greater-than compiler b of
-           One compiler is less-than another if it is preferred over the other."""
+           pkgname. One compiler is less-than another if it is preferred over
+           the other."""
         return self._spec_compare(pkgname, 'compiler', a, b, False, None)

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()
@@ -2196,7 +2242,6 @@ 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
         if self.name != other.name:
@@ -2205,23 +2250,23 @@ def __cmp__(self, other):
         # 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
         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
         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
         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
         if self._dependencies != other._dependencies:
@@ -2230,7 +2275,6 @@ def __cmp__(self, other):
         # 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/__init__.py

@@ -32,15 +32,17 @@
 from spack.test.tally_plugin import Tally
 """Names of tests to be included in Spack's test suite"""
 
-test_names = ['architecture', 'versions', 'url_parse', 'url_substitution', 'packages', 'stage',
+test_names = [
-              'spec_syntax', 'spec_semantics', 'spec_dag', 'concretize',
+    'architecture', 'versions', 'url_parse', 'url_substitution', 'packages',
-              'multimethod', 'install', 'package_sanity', 'config',
+    'stage', 'spec_syntax', 'spec_semantics', 'spec_dag', 'concretize',
-              'directory_layout', 'pattern', 'python_version', 'git_fetch',
+    'multimethod', 'install', 'package_sanity', 'config', 'directory_layout',
-              'svn_fetch', 'hg_fetch', 'mirror', 'modules', 'url_extrapolate',
+    'pattern', 'python_version', 'git_fetch', 'svn_fetch', 'hg_fetch',
-              'cc', 'link_tree', 'spec_yaml', 'optional_deps',
+    'mirror', 'modules', 'url_extrapolate', 'cc', 'link_tree', 'spec_yaml',
-              'make_executable', 'configure_guess', 'lock', 'database',
+    'optional_deps', 'make_executable', 'build_system_guess', 'lock',
-              'namespace_trie', 'yaml', 'sbang', 'environment', 'cmd.find',
+    'database', 'namespace_trie', 'yaml', 'sbang', 'environment', 'cmd.find',
-              'cmd.uninstall', 'cmd.test_install', 'cmd.test_compiler_cmd']
+    'cmd.uninstall', 'cmd.test_install', 'cmd.test_compiler_cmd',
+    'cmd.module'
+]
 
 
 def list_tests():

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()
@@ -50,10 +73,8 @@ def test_dict_functions_for_architecture(self):
         self.assertTrue(isinstance(new_arch.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'):
@@ -110,7 +131,8 @@ def test_user_input_combination(self):
             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)
 

lib/spack/spack/test/build_system_guess.py

@@ -28,14 +28,14 @@
 import unittest
 
 from llnl.util.filesystem import *
-from spack.cmd.create import ConfigureGuesser
+from spack.cmd.create import BuildSystemGuesser
 from spack.stage import Stage
 from spack.test.mock_packages_test import *
 from spack.util.executable import which
 
 
 class InstallTest(unittest.TestCase):
-    """Tests the configure guesser in spack create"""
+    """Tests the build system guesser in spack create"""
 
     def setUp(self):
         self.tar = which('tar')
@@ -44,12 +44,10 @@ def setUp(self):
         os.chdir(self.tmpdir)
         self.stage = None
 
-
     def tearDown(self):
         shutil.rmtree(self.tmpdir, ignore_errors=True)
         os.chdir(self.orig_dir)
 
-
     def check_archive(self, filename, system):
         mkdirp('archive')
         touch(join_path('archive', filename))
@@ -60,24 +58,24 @@ def check_archive(self, filename, system):
         with Stage(url) as stage:
             stage.fetch()
 
-            guesser = ConfigureGuesser()
+            guesser = BuildSystemGuesser()
-            guesser(stage)
+            guesser(stage, url)
             self.assertEqual(system, guesser.build_system)
 
-
-    def test_python(self):
-        self.check_archive('setup.py', 'python')
-
-
     def test_autotools(self):
         self.check_archive('configure', 'autotools')
 
-
     def test_cmake(self):
         self.check_archive('CMakeLists.txt', 'cmake')
 
+    def test_scons(self):
+        self.check_archive('SConstruct', 'scons')
+
+    def test_python(self):
+        self.check_archive('setup.py', 'python')
+
+    def test_R(self):
+        self.check_archive('NAMESPACE', 'R')
 
     def test_unknown(self):
         self.check_archive('foobar', 'unknown')
-
-

lib/spack/spack/test/cmd/find.py

@@ -27,11 +27,7 @@
 import spack.cmd.find
 import unittest
 
-
+from spack.util.pattern import Bunch
-class Bunch(object):
-
-    def __init__(self, **kwargs):
-        self.__dict__.update(kwargs)
 
 
 class FindTest(unittest.TestCase):

lib/spack/spack/test/cmd/module.py

@@ -0,0 +1,83 @@
+##############################################################################
+# 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
+##############################################################################
+import argparse
+import os.path
+
+import spack.cmd.module as module
+import spack.modules as modules
+import spack.test.mock_database
+
+
+class TestModule(spack.test.mock_database.MockDatabase):
+
+    def _get_module_files(self, args):
+        return [
+            modules.module_types[args.module_type](spec).file_name for spec in args.specs  # NOQA: ignore=E501
+        ]
+
+    def test_module_common_operations(self):
+        parser = argparse.ArgumentParser()
+        module.setup_parser(parser)
+        # Try to remove a non existing module [tcl]
+        args = parser.parse_args(['rm', 'doesnotexist'])
+        self.assertRaises(SystemExit, module.module, parser, args)
+        # Remove existing modules [tcl]
+        args = parser.parse_args(['rm', '-y', 'mpileaks'])
+        module_files = self._get_module_files(args)
+        for item in module_files:
+            self.assertTrue(os.path.exists(item))
+        module.module(parser, args)
+        for item in module_files:
+            self.assertFalse(os.path.exists(item))
+        # Add them back [tcl]
+        args = parser.parse_args(['refresh', '-y', 'mpileaks'])
+        module.module(parser, args)
+        for item in module_files:
+            self.assertTrue(os.path.exists(item))
+        # TODO : test the --delete-tree option
+        # TODO : this requires having a separate directory for test modules
+        # Try to find a module with multiple matches
+        args = parser.parse_args(['find', 'mpileaks'])
+        self.assertRaises(SystemExit, module.module, parser, args)
+        # Try to find a module with no matches
+        args = parser.parse_args(['find', 'doesnotexist'])
+        self.assertRaises(SystemExit, module.module, parser, args)
+        # Try to find a module
+        args = parser.parse_args(['find', 'libelf'])
+        module.module(parser, args)
+        # Remove existing modules [dotkit]
+        args = parser.parse_args(['rm', '-y', '-m', 'dotkit', 'mpileaks'])
+        module_files = self._get_module_files(args)
+        for item in module_files:
+            self.assertTrue(os.path.exists(item))
+        module.module(parser, args)
+        for item in module_files:
+            self.assertFalse(os.path.exists(item))
+        # Add them back [dotkit]
+        args = parser.parse_args(['refresh', '-y', '-m', 'dotkit', 'mpileaks'])
+        module.module(parser, args)
+        for item in module_files:
+            self.assertTrue(os.path.exists(item))
+        # TODO : add tests for loads and find to check the prompt format

lib/spack/spack/test/modules.py

@@ -27,7 +27,6 @@
 
 import StringIO
 import spack.modules
-import unittest
 from spack.test.mock_packages_test import MockPackagesTest
 
 FILE_REGISTRY = collections.defaultdict(StringIO.StringIO)
@@ -266,7 +265,7 @@ def test_alter_environment(self):
 
     def test_blacklist(self):
         spack.modules.CONFIGURATION = configuration_blacklist
-        spec = spack.spec.Spec('mpileaks')
+        spec = spack.spec.Spec('mpileaks ^zmpi')
         content = self.get_modulefile_content(spec)
         self.assertEqual(len([x for x in content if 'is-loaded' in x]), 1)
         self.assertEqual(len([x for x in content if 'module load ' in x]), 1)

lib/spack/spack/util/pattern.py

@@ -28,42 +28,50 @@
 
 
 def composite(interface=None, method_list=None, container=list):
-    """
+    """Returns a class decorator that patches a class adding all the methods
-    Returns a class decorator that patches a class adding all the methods it needs to be a composite for a given
+    it needs to be a composite for a given interface.
-    interface.
 
-    :param interface: class exposing the interface to which the composite object must conform. Only non-private and
+    :param interface: class exposing the interface to which the composite
-    non-special methods will be taken into account
+    object must conform. Only non-private and non-special methods will be
+    taken into account
 
     :param method_list: names of methods that should be part of the composite
 
-    :param container: container for the composite object (default = list). Must fulfill the MutableSequence contract.
+    :param container: container for the composite object (default = list).
-    The composite class will expose the container API to manage object composition
+    Must fulfill the MutableSequence contract. The composite class will expose
+    the container API to manage object composition
 
     :return: class decorator
     """
-    # Check if container fulfills the MutableSequence contract and raise an exception if it doesn't
+    # Check if container fulfills the MutableSequence contract and raise an
-    # The patched class returned by the decorator will inherit from the container class to expose the
+    # exception if it doesn't. The patched class returned by the decorator will
-    # interface needed to manage objects composition
+    # inherit from the container class to expose the interface needed to manage
+    # objects composition
     if not issubclass(container, collections.MutableSequence):
         raise TypeError("Container must fulfill the MutableSequence contract")
 
-    # Check if at least one of the 'interface' or the 'method_list' arguments are defined
+    # Check if at least one of the 'interface' or the 'method_list' arguments
+    # are defined
     if interface is None and method_list is None:
-        raise TypeError("Either 'interface' or 'method_list' must be defined on a call to composite")
+        raise TypeError("Either 'interface' or 'method_list' must be defined on a call to composite")  # NOQA : ignore=E501
 
     def cls_decorator(cls):
-        # Retrieve the base class of the composite. Inspect its methods and decide which ones will be overridden
+        # Retrieve the base class of the composite. Inspect its methods and
+        # decide which ones will be overridden
         def no_special_no_private(x):
             return inspect.ismethod(x) and not x.__name__.startswith('_')
 
-        # Patch the behavior of each of the methods in the previous list. This is done associating an instance of the
+        # Patch the behavior of each of the methods in the previous list.
-        # descriptor below to any method that needs to be patched.
+        # This is done associating an instance of the descriptor below to
+        # any method that needs to be patched.
         class IterateOver(object):
+            """Decorator used to patch methods in a composite.
+
+            It iterates over all the items in the instance containing the
+            associated attribute and calls for each of them an attribute
+            with the same name
             """
-            Decorator used to patch methods in a composite. It iterates over all the items in the instance containing the
+
-            associated attribute and calls for each of them an attribute with the same name
-            """
             def __init__(self, name, func=None):
                 self.name = name
                 self.func = func
@@ -72,8 +80,9 @@ def __get__(self, instance, owner):
                 def getter(*args, **kwargs):
                     for item in instance:
                         getattr(item, self.name)(*args, **kwargs)
-                # If we are using this descriptor to wrap a method from an interface, then we must conditionally
+                # If we are using this descriptor to wrap a method from an
-                # use the `functools.wraps` decorator to set the appropriate fields.
+                # interface, then we must conditionally use the
+                # `functools.wraps` decorator to set the appropriate fields
                 if self.func is not None:
                     getter = functools.wraps(self.func)(getter)
                 return getter
@@ -81,7 +90,8 @@ def getter(*args, **kwargs):
         dictionary_for_type_call = {}
         # Construct a dictionary with the methods explicitly passed as name
         if method_list is not None:
-            # python@2.7: method_list_dict = {name: IterateOver(name) for name in method_list}
+            # python@2.7: method_list_dict = {name: IterateOver(name) for name
+            # in method_list}
             method_list_dict = {}
             for name in method_list:
                 method_list_dict[name] = IterateOver(name)
@@ -89,28 +99,40 @@ def getter(*args, **kwargs):
         # Construct a dictionary with the methods inspected from the interface
         if interface is not None:
             ##########
-            # python@2.7: interface_methods = {name: method for name, method in inspect.getmembers(interface, predicate=no_special_no_private)}
+            # python@2.7: interface_methods = {name: method for name, method in
+            # inspect.getmembers(interface, predicate=no_special_no_private)}
             interface_methods = {}
-            for name, method in inspect.getmembers(interface, predicate=no_special_no_private):
+            for name, method in inspect.getmembers(interface, predicate=no_special_no_private):  # NOQA: ignore=E501
                 interface_methods[name] = method
             ##########
-            # python@2.7: interface_methods_dict = {name: IterateOver(name, method) for name, method in interface_methods.iteritems()}
+            # python@2.7: interface_methods_dict = {name: IterateOver(name,
+            # method) for name, method in interface_methods.iteritems()}
             interface_methods_dict = {}
             for name, method in interface_methods.iteritems():
                 interface_methods_dict[name] = IterateOver(name, method)
             ##########
             dictionary_for_type_call.update(interface_methods_dict)
-        # Get the methods that are defined in the scope of the composite class and override any previous definition
+        # Get the methods that are defined in the scope of the composite
+        # class and override any previous definition
         ##########
-        # python@2.7: cls_method = {name: method for name, method in inspect.getmembers(cls, predicate=inspect.ismethod)}
+        # python@2.7: cls_method = {name: method for name, method in
+        # inspect.getmembers(cls, predicate=inspect.ismethod)}
         cls_method = {}
-        for name, method in inspect.getmembers(cls, predicate=inspect.ismethod):
+        for name, method in inspect.getmembers(cls, predicate=inspect.ismethod):  # NOQA: ignore=E501
             cls_method[name] = method
         ##########
         dictionary_for_type_call.update(cls_method)
         # Generate the new class on the fly and return it
         # FIXME : inherit from interface if we start to use ABC classes?
-        wrapper_class = type(cls.__name__, (cls, container), dictionary_for_type_call)
+        wrapper_class = type(cls.__name__, (cls, container),
+                             dictionary_for_type_call)
         return wrapper_class
 
     return cls_decorator
+
+
+class Bunch(object):
+    """Carries a bunch of named attributes (from Alex Martelli bunch)"""
+
+    def __init__(self, **kwargs):
+        self.__dict__.update(kwargs)

share/spack/csh/spack.csh

@@ -74,25 +74,25 @@ case unload:
     # tool's commands to add/remove the result from the environment.
     switch ($_sp_subcommand)
         case "use":
-            set _sp_full_spec = ( "`\spack $_sp_flags module find dotkit $_sp_spec`" )
+            set _sp_full_spec = ( "`\spack $_sp_flags module find --module-type dotkit $_sp_spec`" )
             if ( $? == 0 ) then
                 use $_sp_module_args $_sp_full_spec
             endif
             breaksw
         case "unuse":
-            set _sp_full_spec = ( "`\spack $_sp_flags module find dotkit $_sp_spec`" )
+            set _sp_full_spec = ( "`\spack $_sp_flags module find --module-type dotkit $_sp_spec`" )
             if ( $? == 0 ) then
                 unuse $_sp_module_args $_sp_full_spec
             endif
             breaksw
         case "load":
-            set _sp_full_spec = ( "`\spack $_sp_flags module find tcl $_sp_spec`" )
+            set _sp_full_spec = ( "`\spack $_sp_flags module find --module-type tcl $_sp_spec`" )
             if ( $? == 0 ) then
                 module load $_sp_module_args $_sp_full_spec
             endif
             breaksw
         case "unload":
-            set _sp_full_spec = ( "`\spack $_sp_flags module find tcl $_sp_spec`" )
+            set _sp_full_spec = ( "`\spack $_sp_flags module find --module-type tcl $_sp_spec`" )
             if ( $? == 0 ) then
                 module unload $_sp_module_args $_sp_full_spec
             endif

share/spack/setup-env.sh

@@ -117,19 +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 $_sp_subcommand_args 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 $_sp_subcommand_args 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 $_sp_subcommand_args 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 $_sp_subcommand_args 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/adios/package.py

@@ -12,9 +12,9 @@ class Adios(Package):
     """
 
     homepage = "http://www.olcf.ornl.gov/center-projects/adios/"
-    url = "http://users.nccs.gov/~pnorbert/adios-1.9.0.tar.gz"
+    url = "https://github.com/ornladios/ADIOS/archive/v1.9.0.tar.gz"
 
-    version('1.9.0', 'dbf5cb10e32add2f04c9b4052b7ffa76')
+    version('1.9.0', '310ff02388bbaa2b1c1710ee970b5678')
 
     # Lots of setting up here for this package
     # module swap PrgEnv-intel PrgEnv-$COMP

var/spack/repos/builtin/packages/cdo/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 Cdo(Package):
+    """CDO is a collection of command line Operators to manipulate and analyse
+    Climate and NWP model Data. """
+
+    homepage = "https://code.zmaw.de/projects/cdo"
+    url      = "https://code.zmaw.de/attachments/download/10198/cdo-1.6.9.tar.gz"
+
+    version('1.6.9', 'bf0997bf20e812f35e10188a930e24e2')
+
+    depends_on('netcdf')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+        make()
+        make('install')

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

@@ -30,6 +30,7 @@ class Cmake(Package):
     homepage  = 'https://www.cmake.org'
     url       = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz'
 
+    version('3.6.0',    'aa40fbecf49d99c083415c2411d12db9')
     version('3.5.2',    '701386a1b5ec95f8d1075ecf96383e02')
     version('3.5.1',    'ca051f4a66375c89d1a524e726da0296')
     version('3.5.0',    '33c5d09d4c33d4ffcc63578a6ba8777e')

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

@@ -35,6 +35,7 @@ class Flex(Package):
     version('2.5.39', 'e133e9ead8ec0a58d81166b461244fde')
 
     depends_on("bison", type='build')
+    depends_on("m4", type='build')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)

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/jasper/fix_alpha_channel_assert_fail.patch

@@ -0,0 +1,25 @@
+diff --git a/src/libjasper/jpc/jpc_dec.c b/src/libjasper/jpc/jpc_dec.c
+index fa72a0e..1f4845f 100644
+--- a/src/libjasper/jpc/jpc_dec.c
++++ b/src/libjasper/jpc/jpc_dec.c
+@@ -1069,12 +1069,18 @@ static int jpc_dec_tiledecode(jpc_dec_t *dec, jpc_dec_tile_t *tile)
+	/* Apply an inverse intercomponent transform if necessary. */
+	switch (tile->cp->mctid) {
+	case JPC_MCT_RCT:
+-		assert(dec->numcomps == 3);
++		if (dec->numcomps != 3 && dec->numcomps != 4) {
++			jas_eprintf("bad number of components (%d)\n", dec->numcomps);
++			return -1;
++		}
+		jpc_irct(tile->tcomps[0].data, tile->tcomps[1].data,
+		  tile->tcomps[2].data);
+		break;
+	case JPC_MCT_ICT:
+-		assert(dec->numcomps == 3);
++		if (dec->numcomps != 3 && dec->numcomps != 4) {
++			jas_eprintf("bad number of components (%d)\n", dec->numcomps);
++			return -1;
++		}
+		jpc_iict(tile->tcomps[0].data, tile->tcomps[1].data,
+		  tile->tcomps[2].data);
+		break;

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

@@ -0,0 +1,63 @@
+##############################################################################
+# 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 Jasper(Package):
+    """Library for manipulating JPEG-2000 images"""
+
+    homepage = "https://www.ece.uvic.ca/~frodo/jasper/"
+    url = "https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.1.zip"
+
+    version('1.900.1', 'a342b2b4495b3e1394e161eb5d85d754')
+
+    variant('shared', default=True,
+            description='Builds shared versions of the libraries')
+    variant('debug', default=False,
+            description='Builds debug versions of the libraries')
+
+    depends_on('libjpeg-turbo')
+
+    # Fixes a bug (still in upstream as of v.1.900.1) where an assertion fails
+    # when certain JPEG-2000 files with an alpha channel are processed
+    # see: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=469786
+    patch('fix_alpha_channel_assert_fail.patch')
+
+    def install(self, spec, prefix):
+        configure_options = [
+            '--prefix={0}'.format(prefix),
+            '--mandir={0}'.format(spec.prefix.man),
+        ]
+
+        if '+shared' in spec:
+            configure_options.append('--enable-shared')
+
+        if '+debug' not in spec:
+            configure_options.append('--disable-debug')
+
+        configure(*configure_options)
+
+        make()
+        make('install')

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

@@ -9,7 +9,13 @@ class Mkl(IntelInstaller):
 
     Note: You will have to add the download file to a
     mirror so that Spack can find it. For instructions on how to set up a
-    mirror, see http://software.llnl.gov/spack/mirrors.html"""
+    mirror, see http://software.llnl.gov/spack/mirrors.html.
+
+    To set the threading layer at run time set MKL_THREADING_LAYER
+    variable to one of the following values: INTEL, SEQUENTIAL, PGI.
+    To set interface layer at run time, use set the MKL_INTERFACE_LAYER
+    variable to LP64 or ILP64.
+    """
 
     homepage = "https://software.intel.com/en-us/intel-mkl"
 
@@ -18,6 +24,11 @@ class Mkl(IntelInstaller):
     version('11.3.3.210', 'f72546df27f5ebb0941b5d21fd804e34',
             url="file://%s/l_mkl_11.3.3.210.tgz" % os.getcwd())
 
+    # virtual dependency
+    provides('blas')
+    provides('lapack')
+    # TODO: MKL also provides implementation of Scalapack.
+
     def install(self, spec, prefix):
 
         self.intel_prefix = os.path.join(prefix, "pkg")
@@ -26,3 +37,28 @@ def install(self, spec, prefix):
         mkl_dir = os.path.join(self.intel_prefix, "mkl")
         for f in os.listdir(mkl_dir):
             os.symlink(os.path.join(mkl_dir, f), os.path.join(self.prefix, f))
+
+    def setup_dependent_package(self, module, dspec):
+        # For now use Single Dynamic Library:
+        # To set the threading layer at run time, use the
+        # mkl_set_threading_layer function or set MKL_THREADING_LAYER
+        # variable to one of the following values: INTEL, SEQUENTIAL, PGI.
+        # To set interface layer at run time, use the mkl_set_interface_layer
+        # function or set the MKL_INTERFACE_LAYER variable to LP64 or ILP64.
+
+        # Otherwise one would need to specify several libraries
+        # (e.g. mkl_intel_lp64;mkl_sequential;mkl_core), which reflect
+        # different interface and threading layers.
+
+        name = 'libmkl_rt.%s' % dso_suffix
+        libdir = find_library_path(name, self.prefix.lib64, self.prefix.lib)
+
+        self.spec.blas_shared_lib   = join_path(libdir, name)
+        self.spec.lapack_shared_lib = self.spec.blas_shared_lib
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        # set up MKLROOT for everyone using MKL package
+        spack_env.set('MKLROOT', self.prefix)
+
+    def setup_environment(self, spack_env, env):
+        env.set('MKLROOT', self.prefix)

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

@@ -23,7 +23,10 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os, sys, glob
+import os
+import sys
+import glob
+
 
 class Mumps(Package):
     """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver"""
@@ -44,13 +47,11 @@ class Mumps(Package):
     variant('idx64', default=False, description='Use int64_t/integer*8 as default index type')
     variant('shared', default=True, description='Build shared libraries')
 
-
     depends_on('scotch + esmumps', when='~ptscotch+scotch')
     depends_on('scotch + esmumps + mpi', when='+ptscotch')
     depends_on('metis@5:', when='+metis')
     depends_on('parmetis', when="+parmetis")
     depends_on('blas')
-    depends_on('lapack')
     depends_on('scalapack', when='+mpi')
     depends_on('mpi', when='+mpi')
 
@@ -60,42 +61,52 @@ class Mumps(Package):
     # end before install
     # def patch(self):
     def write_makefile_inc(self):
-        if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec:
+        if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec:  # NOQA: ignore=E501
-            raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi')
+            raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi')  # NOQA: ignore=E501
 
-        makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib]
+        makefile_conf = ["LIBBLAS = %s" % to_link_flags(
+            self.spec['blas'].blas_shared_lib)
+        ]
 
         orderings = ['-Dpord']
 
         if '+ptscotch' in self.spec or '+scotch' in self.spec:
             join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '')
-            makefile_conf.extend(
+            makefile_conf.extend([
-                ["ISCOTCH = -I%s" % self.spec['scotch'].prefix.include,
+                "ISCOTCH = -I%s" % self.spec['scotch'].prefix.include,
                 "LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib,
                                          join_lib,
-                                          join_lib.join(['esmumps', 'scotch', 'scotcherr']))])
+                                         join_lib.join(['esmumps',
+                                                        'scotch',
+                                                        'scotcherr']))
+            ])
+
             orderings.append('-Dscotch')
             if '+ptscotch' in self.spec:
                 orderings.append('-Dptscotch')
 
         if '+parmetis' in self.spec and '+metis' in self.spec:
-            libname = 'parmetis' if '+parmetis' in self.spec else 'metis'
+            makefile_conf.extend([
-            makefile_conf.extend(
+                "IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
-                ["IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
+                "LMETIS = -L%s -l%s -L%s -l%s" % (
-                 "LMETIS = -L%s -l%s -L%s -l%s" % (self.spec['parmetis'].prefix.lib, 'parmetis',self.spec['metis'].prefix.lib, 'metis')])
+                    self.spec['parmetis'].prefix.lib, 'parmetis',
+                    self.spec['metis'].prefix.lib, 'metis')
+            ])
 
             orderings.append('-Dparmetis')
         elif '+metis' in self.spec:
-            makefile_conf.extend(
+            makefile_conf.extend([
-                ["IMETIS = -I%s" % self.spec['metis'].prefix.include,
+                "IMETIS = -I%s" % self.spec['metis'].prefix.include,
-                 "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')])
+                "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')
+            ])
 
             orderings.append('-Dmetis')
 
         makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
 
         # when building shared libs need -fPIC, otherwise
-        # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
+        # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1'
+        # can not be used when making a shared object; recompile with -fPIC
         fpic = '-fPIC' if '+shared' in self.spec else ''
         # TODO: test this part, it needs a full blas, scalapack and
         # partitionning environment with 64bit integers
@@ -104,7 +115,7 @@ def write_makefile_inc(self):
                 # the fortran compilation flags most probably are
                 # working only for intel and gnu compilers this is
                 # perhaps something the compiler should provide
-                ['OPTF    = %s -O  -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),
+                ['OPTF    = %s -O  -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),  # NOQA: ignore=E501
                  'OPTL    = %s -O ' % fpic,
                  'OPTC    = %s -O -DINTSIZE64' % fpic])
         else:
@@ -113,7 +124,6 @@ def write_makefile_inc(self):
                  'OPTL    = %s -O ' % fpic,
                  'OPTC    = %s -O ' % fpic])
 
-
         if '+mpi' in self.spec:
             makefile_conf.extend(
                 ["CC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpicc'),
@@ -134,16 +144,17 @@ def write_makefile_inc(self):
 
         if '+shared' in self.spec:
             if sys.platform == 'darwin':
-                # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew)
+                # Building dylibs with mpif90 causes segfaults on 10.8 and
+                # 10.10. Use gfortran. (Homebrew)
                 makefile_conf.extend([
                     'LIBEXT=.dylib',
-                    'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib),
+                    'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'], prefix.lib),  # NOQA: ignore=E501
                     'RANLIB=echo'
                 ])
             else:
                 makefile_conf.extend([
                     'LIBEXT=.so',
-                    'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,
+                    'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,  # NOQA: ignore=E501
                     'RANLIB=echo'
                 ])
         else:
@@ -153,9 +164,8 @@ def write_makefile_inc(self):
                 'RANLIB = ranlib'
             ])
 
-
+        makefile_inc_template = join_path(
-        makefile_inc_template = join_path(os.path.dirname(self.module.__file__),
+            os.path.dirname(self.module.__file__), 'Makefile.inc')
-                                          'Makefile.inc')
         with open(makefile_inc_template, "r") as fh:
             makefile_conf.extend(fh.read().split('\n'))
 
@@ -164,8 +174,6 @@ def write_makefile_inc(self):
                 makefile_inc = '\n'.join(makefile_conf)
                 fh.write(makefile_inc)
 
-
-
     def install(self, spec, prefix):
         make_libs = []
 
@@ -196,8 +204,8 @@ def install(self, spec, prefix):
             for f in glob.glob(join_path('libseq', '*.h')):
                 install(f, prefix.include)
 
-        # FIXME: extend the tests to mpirun -np 2 (or alike) when build with MPI
+        # FIXME: extend the tests to mpirun -np 2 when build with MPI
-        # FIXME: use something like numdiff to compare blessed output with the current
+        # FIXME: use something like numdiff to compare output files
         with working_dir('examples'):
             if '+float' in spec:
                 os.system('./ssimpletest < input_simpletest_real')

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

@@ -33,6 +33,7 @@ class Netcdf(Package):
     homepage = "http://www.unidata.ucar.edu/software/netcdf"
     url      = "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.tar.gz"
 
+    version('4.4.1', '7843e35b661c99e1d49e60791d5072d8')
     version('4.4.0', 'cffda0cbd97fdb3a06e9274f7aef438e')
     version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae')
 
@@ -47,8 +48,10 @@ class Netcdf(Package):
 
     # Required for NetCDF-4 support
     depends_on("zlib")
-    depends_on("hdf5+mpi", when='+mpi')
+    depends_on('hdf5@:1.8+mpi', when='@:4.4.0+mpi')
-    depends_on("hdf5~mpi", when='~mpi')
+    depends_on('hdf5+mpi', when='@4.4.1:+mpi')
+    depends_on('hdf5@:1.8~mpi', when='@:4.4.0~mpi')
+    depends_on('hdf5~mpi', when='@4.4.1:~mpi')
 
     def install(self, spec, prefix):
         # Environment variables

var/spack/repos/builtin/packages/netlib-scalapack/package.py

@@ -25,8 +25,10 @@
 from spack import *
 import sys
 
+
 class NetlibScalapack(Package):
-    """ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines"""
+    """ScaLAPACK is a library of high-performance linear algebra routines for
+    parallel distributed memory machines"""
 
     homepage = "http://www.netlib.org/scalapack/"
     url      = "http://www.netlib.org/scalapack/scalapack-2.0.2.tgz"
@@ -48,11 +50,23 @@ class NetlibScalapack(Package):
 
     def install(self, spec, prefix):
         options = [
-            "-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else 'OFF'),
+            "-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else
-            "-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else 'ON'),
+                                             'OFF'),
-            "-DUSE_OPTIMIZED_LAPACK_BLAS:BOOL=ON", # forces scalapack to use find_package(LAPACK)
+            "-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else
+                                             'ON'),
+            # forces scalapack to use find_package(LAPACK):
+            "-DUSE_OPTIMIZED_LAPACK_BLAS:BOOL=ON",
         ]
 
+        # Make sure we use Spack's Lapack:
+        options.extend([
+            '-DLAPACK_FOUND=true',
+            '-DLAPACK_INCLUDE_DIRS=%s' % spec['lapack'].prefix.include,
+            '-DLAPACK_LIBRARIES=%s' % (
+                spec['lapack'].lapack_shared_lib if '+shared' in spec else
+                spec['lapack'].lapack_static_lib),
+        ])
+
         if '+fpic' in spec:
             options.extend([
                 "-DCMAKE_C_FLAGS=-fPIC",
@@ -66,16 +80,15 @@ def install(self, spec, prefix):
             make()
             make("install")
 
-        # The shared libraries are not installed correctly on Darwin; correct this
+        # The shared libraries are not installed correctly on Darwin:
         if (sys.platform == 'darwin') and ('+shared' in spec):
             fix_darwin_install_name(prefix.lib)
 
-
     def setup_dependent_package(self, module, dependent_spec):
         spec = self.spec
-        lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
+        lib_suffix = dso_suffix if '+shared' in spec else 'a'
-        lib_suffix = lib_dsuffix if '+shared' in spec else '.a'
 
         spec.fc_link = '-L%s -lscalapack' % spec.prefix.lib
         spec.cc_link = spec.fc_link
-        spec.libraries = [join_path(spec.prefix.lib, 'libscalapack%s' % lib_suffix)]
+        spec.libraries = [join_path(spec.prefix.lib,
+                                    'libscalapack.%s' % lib_suffix)]

var/spack/repos/builtin/packages/py-h5py/package.py

@@ -46,6 +46,7 @@ class PyH5py(Package):
     depends_on('hdf5@1.8.4:')
     depends_on('hdf5+mpi', when='+mpi')
     depends_on('mpi', when='+mpi')
+    depends_on('py-mpi4py', when='+mpi')
 
     # Build and runtime dependencies
     depends_on('py-numpy@1.6.1:', type=nolink)

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

@@ -44,6 +44,7 @@ class PyNumpy(Package):
 
     extends('python')
     depends_on('py-nose', type='build')
+    depends_on('py-setuptools', type='build')
     depends_on('blas',   when='+blas')
     depends_on('lapack', when='+lapack')
 

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

@@ -53,6 +53,7 @@ class Python(Package):
 
     extendable = True
 
+    variant('tk',   default=False, description='Provide support for Tkinter')
     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
@@ -68,6 +69,8 @@ class Python(Package):
     depends_on("ncurses")
     depends_on("sqlite")
     depends_on("zlib")
+    depends_on("tk",  when="+tk")
+    depends_on("tcl", when="+tk")
 
     def install(self, spec, prefix):
         # Need this to allow python build to find the Python installation.
@@ -77,24 +80,32 @@ def install(self, spec, prefix):
         # Rest of install is pretty standard except setup.py needs to
         # be able to read the CPPFLAGS and LDFLAGS as it scans for the
         # library and headers to build
-        cppflags = ' -I'.join([
+        include_dirs = [
             spec['openssl'].prefix.include,  spec['bzip2'].prefix.include,
             spec['readline'].prefix.include, spec['ncurses'].prefix.include,
             spec['sqlite'].prefix.include,   spec['zlib'].prefix.include
-        ])
+        ]
 
-        ldflags = ' -L'.join([
+        library_dirs = [
             spec['openssl'].prefix.lib,  spec['bzip2'].prefix.lib,
             spec['readline'].prefix.lib, spec['ncurses'].prefix.lib,
             spec['sqlite'].prefix.lib,   spec['zlib'].prefix.lib
+        ]
+
+        if '+tk' in spec:
+            include_dirs.extend([
+                spec['tk'].prefix.include, spec['tcl'].prefix.include
+            ])
+            library_dirs.extend([
+                spec['tk'].prefix.lib, spec['tcl'].prefix.lib
             ])
 
         config_args = [
             "--prefix={0}".format(prefix),
             "--with-threads",
             "--enable-shared",
-            "CPPFLAGS=-I{0}".format(cppflags),
+            "CPPFLAGS=-I{0}".format(" -I".join(include_dirs)),
-            "LDFLAGS=-L{0}".format(ldflags)
+            "LDFLAGS=-L{0}".format(" -L".join(library_dirs))
         ]
 
         if '+ucs4' in spec:
@@ -116,6 +127,25 @@ def install(self, spec, prefix):
 
         self.filter_compilers(spec, prefix)
 
+    # TODO: Once better testing support is integrated, add the following tests
+    # https://wiki.python.org/moin/TkInter
+    #
+    #    if '+tk' in spec:
+    #        env['TK_LIBRARY']  = join_path(spec['tk'].prefix.lib,
+    #            'tk{0}'.format(spec['tk'].version.up_to(2)))
+    #        env['TCL_LIBRARY'] = join_path(spec['tcl'].prefix.lib,
+    #            'tcl{0}'.format(spec['tcl'].version.up_to(2)))
+    #
+    #        $ python
+    #        >>> import _tkinter
+    #
+    #        if spec.satisfies('@3:')
+    #            >>> import tkinter
+    #            >>> tkinter._test()
+    #        else:
+    #            >>> import Tkinter
+    #            >>> Tkinter._test()
+
     def filter_compilers(self, spec, prefix):
         """Run after install to tell the configuration files and Makefiles
         to use the compilers that Spack built the package with.

var/spack/repos/builtin/packages/suite-sparse/package.py

@@ -32,21 +32,20 @@ class SuiteSparse(Package):
     homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html'
     url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz'
 
-    version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319')
     version('4.5.3', '8ec57324585df3c6483ad7f556afccbd')
+    version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319')
 
-    # FIXME: (see below)
+    variant('tbb', default=True, description='Build with Intel TBB')
-    # variant('tbb', default=True, description='Build with Intel TBB')
 
     depends_on('blas')
     depends_on('lapack')
 
     depends_on('metis@5.1.0', when='@4.5.1:')
-    # FIXME:
     # in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng
     # flags does not seem to be used, which leads to linking errors on Linux.
-    # Try re-enabling in future versions.
+    depends_on('tbb', when='@4.5.3:+tbb')
-    # depends_on('tbb', when='+tbb')
+
+    patch('tbb_453.patch', when='@4.5.3')
 
     def install(self, spec, prefix):
         # The build system of SuiteSparse is quite old-fashioned.
@@ -73,20 +72,24 @@ def install(self, spec, prefix):
         ])
 
         # Intel TBB in SuiteSparseQR
-        if '+tbb' in spec:
+        if 'tbb' in spec:
             make_args.extend([
                 'SPQR_CONFIG=-DHAVE_TBB',
                 'TBB=-L%s -ltbb' % spec['tbb'].prefix.lib,
             ])
 
-        # BLAS arguments require path to libraries
+        # Make sure Spack's Blas/Lapack is used. Otherwise System's
-        # FIXME: (blas/lapack always provide libblas and liblapack as aliases)
+        # Blas/Lapack might be picked up.
+        blas = to_link_flags(spec['blas'].blas_shared_lib)
+        lapack = to_link_flags(spec['lapack'].lapack_shared_lib)
         if '@4.5.1' in spec:
             # adding -lstdc++ is clearly an ugly way to do this, but it follows
             # with the TCOV path of SparseSuite 4.5.1's Suitesparse_config.mk
+            blas += ' -lstdc++'
+
         make_args.extend([
-                'BLAS=-lblas -lstdc++',
+            'BLAS=%s' % blas,
-                'LAPACK=-llapack'
+            'LAPACK=%s' % lapack
         ])
 
         make('install', *make_args)

var/spack/repos/builtin/packages/suite-sparse/tbb_453.patch

@@ -0,0 +1,13 @@
+diff --git a/SPQR/Lib/Makefile b/SPQR/Lib/Makefile
+index eaade58..d0de852 100644
+--- a/SPQR/Lib/Makefile
++++ b/SPQR/Lib/Makefile
+@@ -13,7 +13,7 @@ ccode: all
+ include ../../SuiteSparse_config/SuiteSparse_config.mk
+ 
+ # SPQR depends on CHOLMOD, AMD, COLAMD, LAPACK, the BLAS and SuiteSparse_config
+-LDLIBS += -lamd -lcolamd -lcholmod -lsuitesparseconfig $(LAPACK) $(BLAS)
++LDLIBS += -lamd -lcolamd -lcholmod -lsuitesparseconfig $(TBB) $(LAPACK) $(BLAS)
+ 
+ # compile and install in SuiteSparse/lib
+ library:

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

@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Tcl(Package):
     """Tcl (Tool Command Language) is a very powerful but easy to
        learn dynamic programming language, suitable for a very wide
@@ -34,9 +35,6 @@ class Tcl(Package):
        extensible."""
     homepage = "http://www.tcl.tk"
 
-    def url_for_version(self, version):
-        return 'http://prdownloads.sourceforge.net/tcl/tcl%s-src.tar.gz' % version
-
     version('8.6.5', '0e6426a4ca9401825fbc6ecf3d89a326')
     version('8.6.4', 'd7cbb91f1ded1919370a30edd1534304')
     version('8.6.3', 'db382feca91754b7f93da16dc4cdad1f')
@@ -44,8 +42,18 @@ def url_for_version(self, version):
 
     depends_on('zlib')
 
+    def url_for_version(self, version):
+        base_url = 'http://prdownloads.sourceforge.net/tcl'
+        return '{0}/tcl{1}-src.tar.gz'.format(base_url, version)
+
+    def setup_environment(self, spack_env, env):
+        # When using Tkinter from within spack provided python+tk, python
+        # will not be able to find Tcl/Tk unless TCL_LIBRARY is set.
+        env.set('TCL_LIBRARY', join_path(self.prefix.lib, 'tcl{0}'.format(
+                self.spec.version.up_to(2))))
+
     def install(self, spec, prefix):
         with working_dir('unix'):
-            configure("--prefix=%s" % prefix)
+            configure("--prefix={0}".format(prefix))
             make()
             make("install")

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

@@ -24,11 +24,13 @@
 ##############################################################################
 from spack import *
 
+
 class TheSilverSearcher(Package):
     """Fast recursive grep alternative"""
     homepage = "http://geoff.greer.fm/ag/"
-    url      = "http://geoff.greer.fm/ag/releases/the_silver_searcher-0.30.0.tar.gz"
+    url      = "http://geoff.greer.fm/ag/releases/the_silver_searcher-0.32.0.tar.gz"
 
+    version('0.32.0', '3fdfd5836924246073d5344257a06823')
     version('0.30.0', '95e2e7859fab1156c835aff7413481db')
 
     depends_on('pcre')

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

@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Tk(Package):
     """Tk is a graphical user interface toolkit that takes developing
        desktop applications to a higher level than conventional
@@ -33,16 +34,24 @@ class Tk(Package):
        and more."""
     homepage = "http://www.tcl.tk"
 
-    def url_for_version(self, version):
+    version('8.6.5', '11dbbd425c3e0201f20d6a51482ce6c4')
-        return "http://prdownloads.sourceforge.net/tcl/tk%s-src.tar.gz" % version
-
     version('8.6.3', '85ca4dbf4dcc19777fd456f6ee5d0221')
 
     depends_on("tcl")
 
+    def url_for_version(self, version):
+        base_url = "http://prdownloads.sourceforge.net/tcl"
+        return "{0}/tk{1}-src.tar.gz".format(base_url, version)
+
+    def setup_environment(self, spack_env, env):
+        # When using Tkinter from within spack provided python+tk, python
+        # will not be able to find Tcl/Tk unless TK_LIBRARY is set.
+        env.set('TK_LIBRARY', join_path(self.prefix.lib, 'tk{0}'.format(
+                self.spec.version.up_to(2))))
+
     def install(self, spec, prefix):
         with working_dir('unix'):
-            configure("--prefix=%s" % prefix,
+            configure("--prefix={0}".format(prefix),
-                      "--with-tcl=%s" % spec['tcl'].prefix.lib)
+                      "--with-tcl={0}".format(spec['tcl'].prefix.lib))
             make()
             make("install")

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',