From 1ad474f1a9afa7ccc8d596caa08278e19a69eb97 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 30 Jul 2014 23:30:07 -0700
Subject: [PATCH 01/71] Allow per-version URLs instead of one single URL per
 package.

---
 lib/spack/llnl/util/lang.py                   |  15 +-
 lib/spack/spack/__init__.py                   |   4 +-
 lib/spack/spack/cmd/create.py                 |  16 +--
 lib/spack/spack/cmd/edit.py                   |   2 +-
 lib/spack/spack/concretize.py                 |  10 +-
 lib/spack/spack/package.py                    | 133 ++++++++++++------
 lib/spack/spack/relations.py                  |  30 +++-
 lib/spack/spack/test/package_sanity.py        |  30 +++-
 lib/spack/spack/url.py                        |  24 ++--
 lib/spack/spack/util/compression.py           |   2 +-
 lib/spack/spack/version.py                    |   2 +-
 var/spack/mock_packages/callpath/package.py   |   6 +-
 .../mock_packages/direct_mpich/package.py     |   2 +-
 var/spack/mock_packages/dyninst/package.py    |   5 +-
 var/spack/mock_packages/fake/package.py       |   3 +-
 .../mock_packages/indirect_mpich/package.py   |   2 +-
 var/spack/mock_packages/libdwarf/package.py   |   8 +-
 var/spack/mock_packages/libelf/package.py     |   6 +-
 var/spack/mock_packages/mpich/package.py      |  10 +-
 var/spack/mock_packages/mpich2/package.py     |  12 +-
 var/spack/mock_packages/mpileaks/package.py   |   8 +-
 .../trivial_install_test_package/package.py   |   2 +-
 var/spack/mock_packages/zmpi/package.py       |   2 +-
 var/spack/packages/SAMRAI/package.py          |  20 ++-
 var/spack/packages/boost/package.py           |  51 ++++---
 var/spack/packages/cmake/package.py           |   3 +-
 var/spack/packages/dyninst/package.py         |   4 +-
 var/spack/packages/graphlib/package.py        |   2 +-
 var/spack/packages/hdf5/package.py            |   4 +-
 var/spack/packages/launchmon/package.py       |   2 +-
 var/spack/packages/libdwarf/package.py        |   6 +-
 var/spack/packages/libelf/package.py          |   4 +-
 var/spack/packages/libevent/package.py        |  23 ++-
 var/spack/packages/libunwind/package.py       |   2 +-
 var/spack/packages/mpich/package.py           |   2 +-
 var/spack/packages/mrnet/package.py           |   5 +-
 var/spack/packages/mvapich2/package.py        |   7 +-
 var/spack/packages/ncurses/package.py         |   6 +-
 var/spack/packages/openmpi/package.py         |   2 +-
 var/spack/packages/parmetis/package.py        |   2 +-
 var/spack/packages/pmgr_collective/package.py |   2 +-
 var/spack/packages/scr/package.py             |   2 +-
 var/spack/packages/spindle/package.py         |   2 +-
 var/spack/packages/stat/package.py            |   4 +-
 var/spack/packages/tau/package.py             |   3 +-
 var/spack/packages/tmux/package.py            |   2 +-
 var/spack/packages/vim/package.py             |  24 ++--
 var/spack/packages/zlib/package.py            |   2 +-
 48 files changed, 312 insertions(+), 208 deletions(-)

diff --git a/lib/spack/llnl/util/lang.py b/lib/spack/llnl/util/lang.py
index 7590fb12989..ce7d0197f02 100644
--- a/lib/spack/llnl/util/lang.py
+++ b/lib/spack/llnl/util/lang.py
@@ -119,9 +119,8 @@ def caller_locals():
 
 
 def get_calling_package_name():
-    """Make sure that the caller is a class definition, and return
-       the module's name.  This is useful for getting the name of
-       spack packages from inside a relation function.
+    """Make sure that the caller is a class definition, and return the
+       module's name.
     """
     stack = inspect.stack()
     try:
@@ -144,8 +143,9 @@ def get_calling_package_name():
 def attr_required(obj, attr_name):
     """Ensure that a class has a required attribute."""
     if not hasattr(obj, attr_name):
-        tty.die("No required attribute '%s' in class '%s'"
-                % (attr_name, obj.__class__.__name__))
+        raise RequiredAttributeError(
+            "No required attribute '%s' in class '%s'"
+            % (attr_name, obj.__class__.__name__))
 
 
 def attr_setdefault(obj, name, value):
@@ -259,3 +259,8 @@ def in_function(function_name):
         return False
     finally:
         del stack
+
+
+class RequiredAttributeError(ValueError):
+    def __init__(self, message):
+        super(RequiredAttributeError, self).__init__(message)
diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py
index d0cf8804ba7..50fe453cfb7 100644
--- a/lib/spack/spack/__init__.py
+++ b/lib/spack/spack/__init__.py
@@ -32,7 +32,7 @@
 # TODO: maybe this should be separated out and should go in build_environment.py?
 # TODO: it's not clear where all the stuff that needs to be included in packages
 #       should live.  This file is overloaded for spack core vs. for packages.
-__all__ = ['Package', 'when', 'provides', 'depends_on',
+__all__ = ['Package', 'when', 'provides', 'depends_on', 'version',
            'patch', 'Version', 'working_dir', 'which', 'Executable',
            'filter_file', 'change_sed_delimiter']
 
@@ -146,6 +146,6 @@
 #
 from llnl.util.filesystem import working_dir
 from spack.package import Package
-from spack.relations import depends_on, provides, patch
+from spack.relations import *
 from spack.multimethod import when
 from spack.version import Version
diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py
index cc9a1342e74..1a1a19a4b62 100644
--- a/lib/spack/spack/cmd/create.py
+++ b/lib/spack/spack/cmd/create.py
@@ -70,7 +70,7 @@ class ${class_name}(Package):
     homepage = "http://www.example.com"
     url      = "${url}"
 
-    versions = ${versions}
+${versions}
 
     def install(self, spec, prefix):
         # FIXME: Modify the configure line to suit your build system here.
@@ -114,13 +114,11 @@ def __call__(self, stage):
             self.configure = '%s\n        # %s' % (autotools, cmake)
 
 
-def make_version_dict(ver_hash_tuples):
-    max_len = max(len(str(v)) for v,hfg in ver_hash_tuples)
-    width = max_len + 2
-    format = "%-" + str(width) + "s : '%s',"
-    sep = '\n                 '
-    return '{ ' + sep.join(format % ("'%s'" % v, h)
-                           for v, h in ver_hash_tuples) + ' }'
+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 get_name():
@@ -195,7 +193,7 @@ def create(parser, args):
                 configure=guesser.configure,
                 class_name=mod_to_class(name),
                 url=url,
-                versions=make_version_dict(ver_hash_tuples)))
+                versions=make_version_calls(ver_hash_tuples)))
 
     # If everything checks out, go ahead and edit.
     spack.editor(pkg_path)
diff --git a/lib/spack/spack/cmd/edit.py b/lib/spack/spack/cmd/edit.py
index c96cf75c9bc..3647186a3cd 100644
--- a/lib/spack/spack/cmd/edit.py
+++ b/lib/spack/spack/cmd/edit.py
@@ -44,7 +44,7 @@ class ${class_name}(Package):
     homepage = "http://www.example.com"
     url      = "http://www.example.com/${name}-1.0.tar.gz"
 
-    versions = { '1.0' : '0123456789abcdef0123456789abcdef' }
+    version('1.0', '0123456789abcdef0123456789abcdef')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py
index f5775ef1bfc..eb497711b72 100644
--- a/lib/spack/spack/concretize.py
+++ b/lib/spack/spack/concretize.py
@@ -72,7 +72,7 @@ def concretize_version(self, spec):
         if valid_versions:
             spec.versions = ver([valid_versions[-1]])
         else:
-            spec.versions = ver([pkg.default_version])
+            raise NoValidVerionError(spec)
 
 
     def concretize_architecture(self, spec):
@@ -158,3 +158,11 @@ def __init__(self, compiler_spec):
         super(UnavailableCompilerVersionError, self).__init__(
             "No available compiler version matches '%s'" % compiler_spec,
             "Run 'spack compilers' to see available compiler Options.")
+
+
+class NoValidVerionError(spack.error.SpackError):
+    """Raised when there is no available version for a package that
+       satisfies a spec."""
+    def __init__(self, spec):
+        super(NoValidVerionError, self).__init__(
+            "No available version of %s matches '%s'" % (spec.name, spec.versions))
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 79a6c2362eb..90e77b5e826 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -296,9 +296,12 @@ class SomePackage(Package):
     """
 
     #
-    # These variables are defaults for the various relations defined on
-    # packages.  Subclasses will have their own versions of these.
+    # These variables are defaults for the various "relations".
     #
+    """Map of information about Versions of this package.
+       Map goes: Version -> VersionDescriptor"""
+    versions = {}
+
     """Specs of dependency packages, keyed by name."""
     dependencies = {}
 
@@ -317,16 +320,10 @@ class SomePackage(Package):
     """By default we build in parallel.  Subclasses can override this."""
     parallel = True
 
-    """Dirty hack for forcing packages with uninterpretable URLs
-       TODO: get rid of this.
-    """
-    force_url = False
-
 
     def __init__(self, spec):
         # These attributes are required for all packages.
         attr_required(self.__class__, 'homepage')
-        attr_required(self.__class__, 'url')
 
         # this determines how the package should be built.
         self.spec = spec
@@ -337,24 +334,32 @@ def __init__(self, spec):
         if '.' in self.name:
             self.name = self.name[self.name.rindex('.') + 1:]
 
-        # Make sure URL is an allowed type
-        validate_package_url(self.url)
-
-        # patch up the URL with a new version if the spec version is concrete
-        if self.spec.versions.concrete:
-            self.url = self.url_for_version(self.spec.version)
-
         # This is set by scraping a web page.
         self._available_versions = None
 
-        # versions should be a dict from version to checksum, for safe versions
-        # of this package.  If it's not present, make it an empty dict.
-        if not hasattr(self, 'versions'):
-            self.versions = {}
+        # Sanity check some required variables that could be
+        # overridden by package authors.
+        def sanity_check_dict(attr_name):
+            if not hasattr(self, attr_name):
+                raise PackageError("Package %s must define %s" % attr_name)
 
-        if not isinstance(self.versions, dict):
-            raise ValueError("versions attribute of package %s must be a dict!"
-                             % self.name)
+            attr = getattr(self, attr_name)
+            if not isinstance(attr, dict):
+                raise PackageError("Package %s has non-dict %s attribute!"
+                                   % (self.name, attr_name))
+        sanity_check_dict('versions')
+        sanity_check_dict('dependencies')
+        sanity_check_dict('conflicted')
+        sanity_check_dict('patches')
+
+        # Check versions in the versions dict.
+        for v in self.versions:
+            assert(isinstance(v, Version))
+
+        # Check version descriptors
+        for v in sorted(self.versions):
+            vdesc = self.versions[v]
+            assert(isinstance(vdesc, spack.relations.VersionDescriptor))
 
         # Version-ize the keys in versions dict
         try:
@@ -366,6 +371,10 @@ def __init__(self, spec):
         # stage used to build this package.
         self._stage = None
 
+        # patch up self.url based on the actual version
+        if self.spec.concrete:
+            self.url = self.url_for_version(self.version)
+
         # Set a default list URL (place to find available versions)
         if not hasattr(self, 'list_url'):
             self.list_url = None
@@ -374,18 +383,6 @@ def __init__(self, spec):
             self.list_depth = 1
 
 
-    @property
-    def default_version(self):
-        """Get the version in the default URL for this package,
-           or fails."""
-        try:
-            return url.parse_version(self.__class__.url)
-        except UndetectableVersionError:
-            raise PackageError(
-                "Couldn't extract a default version from %s." % self.url,
-                " You must specify it explicitly in the package file.")
-
-
     @property
     def version(self):
         if not self.spec.concrete:
@@ -514,16 +511,50 @@ def url_version(self, version):
            override this, e.g. for boost versions where you need to ensure that there
            are _'s in the download URL.
         """
-        if self.force_url:
-            return self.default_version
         return str(version)
 
 
     def url_for_version(self, version):
-        """Gives a URL that you can download a new version of this package from."""
-        if self.force_url:
-            return self.url
-        return url.substitute_version(self.__class__.url, self.url_version(version))
+        """Returns a URL that you can download a new version of this package from."""
+        if not isinstance(version, Version):
+            version = Version(version)
+
+        def nearest_url(version):
+            """Finds the URL for the next lowest version with a URL.
+               If there is no lower version with a URL, uses the
+               package url property. If that isn't there, uses a
+               *higher* URL, and if that isn't there raises an error.
+            """
+            url = getattr(self, 'url', None)
+            for v in sorted(self.versions):
+                if v > version and url:
+                    break
+                if self.versions[v].url:
+                    url = self.versions[v].url
+            if not url:
+                raise PackageVersionError(v)
+            return url
+
+        if version in self.versions:
+            vdesc = self.versions[version]
+            if not vdesc.url:
+                base_url = nearest_url(version)
+                vdesc.url = url.substitute_version(
+                    base_url, self.url_version(version))
+            return vdesc.url
+        else:
+            return nearest_url(version)
+
+
+    @property
+    def default_url(self):
+        if self.concrete:
+            return self.url_for_version(self.version)
+        else:
+            url = getattr(self, 'url', None)
+            if url:
+                return url
+
 
 
     def remove_prefix(self):
@@ -548,7 +579,7 @@ def do_fetch(self):
         self.stage.fetch()
 
         if spack.do_checksum and self.version in self.versions:
-            digest = self.versions[self.version]
+            digest = self.versions[self.version].checksum
             self.stage.check(digest)
             tty.msg("Checksum passed for %s@%s" % (self.name, self.version))
 
@@ -779,6 +810,9 @@ def do_clean_dist(self):
 
 
     def fetch_available_versions(self):
+        if not hasattr(self, 'url'):
+            raise VersionFetchError(self.__class__)
+
         # If not, then try to fetch using list_url
         if not self._available_versions:
             try:
@@ -865,7 +899,6 @@ def print_pkg(message):
     print message
 
 
-
 class FetchError(spack.error.SpackError):
     """Raised when something goes wrong during fetch."""
     def __init__(self, message, long_msg=None):
@@ -889,3 +922,19 @@ class InvalidPackageDependencyError(PackageError):
        its dependencies."""
     def __init__(self, message):
         super(InvalidPackageDependencyError, self).__init__(message)
+
+
+class PackageVersionError(PackageError):
+    """Raised when a version URL cannot automatically be determined."""
+    def __init__(self, version):
+        super(PackageVersionError, self).__init__(
+            "Cannot determine a URL automatically for version %s." % version,
+            "Please provide a url for this version in the package.py file.")
+
+
+class VersionFetchError(PackageError):
+    """Raised when a version URL cannot automatically be determined."""
+    def __init__(self, cls):
+        super(VersionFetchError, self).__init__(
+            "Cannot fetch version for package %s " % cls.__name__ +
+            "because it does not define a default url.")
diff --git a/lib/spack/spack/relations.py b/lib/spack/spack/relations.py
index f46b7dfc84d..a7b46cfb331 100644
--- a/lib/spack/spack/relations.py
+++ b/lib/spack/spack/relations.py
@@ -68,6 +68,8 @@ class Mpileaks(Package):
         spack install mpileaks ^mvapich
         spack install mpileaks ^mpich
 """
+__all__ = [ 'depends_on', 'provides', 'patch', 'version' ]
+
 import re
 import inspect
 import importlib
@@ -77,14 +79,38 @@ class Mpileaks(Package):
 import spack
 import spack.spec
 import spack.error
+import spack.url
 
+from spack.version import Version
 from spack.patch import Patch
 from spack.spec import Spec, parse_anonymous_spec
 
 
-"""Adds a dependencies local variable in the locals of
-   the calling class, based on args. """
+class VersionDescriptor(object):
+    """A VersionDescriptor contains information to describe a
+       particular version of a package.  That currently includes a URL
+       for the version along with a checksum."""
+    def __init__(self, checksum, url):
+        self.checksum = checksum
+        self.url = url
+
+
+def version(ver, checksum, **kwargs):
+    """Adds a version and associated metadata to the package."""
+    pkg = caller_locals()
+
+    versions = pkg.setdefault('versions', {})
+    patches  = pkg.setdefault('patches', {})
+
+    ver = Version(ver)
+    url = kwargs.get('url', None)
+
+    versions[ver] = VersionDescriptor(checksum, url)
+
+
 def depends_on(*specs):
+    """Adds a dependencies local variable in the locals of
+       the calling class, based on args. """
     pkg = get_calling_package_name()
 
     dependencies = caller_locals().setdefault('dependencies', {})
diff --git a/lib/spack/spack/test/package_sanity.py b/lib/spack/spack/test/package_sanity.py
index 1a7bc5dc5e8..e3de6950702 100644
--- a/lib/spack/spack/test/package_sanity.py
+++ b/lib/spack/spack/test/package_sanity.py
@@ -29,19 +29,35 @@
 
 import spack
 import spack.url as url
+from spack.packages import PackageDB
+
 
 class PackageSanityTest(unittest.TestCase):
 
-    def test_get_all_packages(self):
-        """Get all packages once and make sure that works."""
+    def check_db(self):
+        """Get all packages in a DB to make sure they work."""
         for name in spack.db.all_package_names():
             spack.db.get(name)
 
 
+    def test_get_all_packages(self):
+        """Get all packages once and make sure that works."""
+        self.check_db()
+
+
+    def test_get_all_mock_packages(self):
+        """Get the mock packages once each too."""
+        tmp = spack.db
+        spack.db = PackageDB(spack.mock_packages_path)
+        self.check_db()
+        spack.db = tmp
+
+
     def test_url_versions(self):
-        """Ensure that url_for_version does the right thing for at least the
-           default version of each package.
-        """
+        """Check URLs for regular packages, if they are explicitly defined."""
         for pkg in spack.db.all_packages():
-            v = url.parse_version(pkg.url)
-            self.assertEqual(pkg.url, pkg.url_for_version(v))
+            for v, vdesc in pkg.versions.items():
+                if vdesc.url:
+                    # If there is a url for the version check it.
+                    v_url = pkg.url_for_version(v)
+                    self.assertEqual(vdesc.url, v_url)
diff --git a/lib/spack/spack/url.py b/lib/spack/spack/url.py
index 1b8120168f2..902ce9817d8 100644
--- a/lib/spack/spack/url.py
+++ b/lib/spack/spack/url.py
@@ -82,12 +82,16 @@ def parse_version_string_with_indices(path):
     """Try to extract a version string from a filename or URL.  This is taken
        largely from Homebrew's Version class."""
 
-    if os.path.isdir(path):
-        stem = os.path.basename(path)
-    elif re.search(r'((?:sourceforge.net|sf.net)/.*)/download$', path):
-        stem = comp.stem(os.path.dirname(path))
-    else:
-        stem = comp.stem(path)
+    # Strip off sourceforge download stuffix.
+    if re.search(r'((?:sourceforge.net|sf.net)/.*)/download$', path):
+        path = os.path.dirname(path)
+
+    # Strip archive extension
+    path = comp.strip_extension(path)
+
+    # Take basename to avoid including parent dirs in version name
+    # Remember the offset of the stem in the full path.
+    stem = os.path.basename(path)
 
     version_types = [
         # GitHub tarballs, e.g. v1.2.3
@@ -137,10 +141,10 @@ def parse_version_string_with_indices(path):
         (r'_((\d+\.)+\d+[a-z]?)[.]orig$', stem),
 
         # e.g. http://www.openssl.org/source/openssl-0.9.8s.tar.gz
-        (r'-([^-]+)', stem),
+        (r'-([^-]+(-alpha|-beta)?)', stem),
 
         # e.g. astyle_1.23_macosx.tar.gz
-        (r'_([^_]+)', stem),
+        (r'_([^_]+(_alpha|_beta)?)', stem),
 
         # e.g. http://mirrors.jenkins-ci.org/war/1.486/jenkins.war
         (r'\/(\d\.\d+)\/', path),
@@ -152,7 +156,9 @@ def parse_version_string_with_indices(path):
         regex, match_string = vtype[:2]
         match = re.search(regex, match_string)
         if match and match.group(1) is not None:
-            return match.group(1), match.start(1), match.end(1)
+            version = match.group(1)
+            start = path.index(version)
+            return version, start, start+len(version)
 
     raise UndetectableVersionError(path)
 
diff --git a/lib/spack/spack/util/compression.py b/lib/spack/spack/util/compression.py
index 7ce8e8c65b8..a67576bd508 100644
--- a/lib/spack/spack/util/compression.py
+++ b/lib/spack/spack/util/compression.py
@@ -48,7 +48,7 @@ def decompressor_for(path):
     return tar
 
 
-def stem(path):
+def strip_extension(path):
     """Get the part of a path that does not include its compressed
        type extension."""
     for type in ALLOWED_ARCHIVE_TYPES:
diff --git a/lib/spack/spack/version.py b/lib/spack/spack/version.py
index ce94303a9c6..4558f883843 100644
--- a/lib/spack/spack/version.py
+++ b/lib/spack/spack/version.py
@@ -181,7 +181,7 @@ def a_or_n(seg):
 
         # Add possible alpha or beta indicator at the end of each segemnt
         # We treat these specially b/c they're so common.
-        wc += '[ab]?)?' * (len(segments) - 1)
+        wc += '(?:[a-z]|alpha|beta)?)?' * (len(segments) - 1)
         return wc
 
 
diff --git a/var/spack/mock_packages/callpath/package.py b/var/spack/mock_packages/callpath/package.py
index b4fd0f44825..5b6b70ba2a5 100644
--- a/var/spack/mock_packages/callpath/package.py
+++ b/var/spack/mock_packages/callpath/package.py
@@ -28,9 +28,9 @@ class Callpath(Package):
     homepage = "https://github.com/tgamblin/callpath"
     url      = "http://github.com/tgamblin/callpath-1.0.tar.gz"
 
-    versions = { 0.8 : 'foobarbaz',
-                 0.9 : 'foobarbaz',
-                 1.0 : 'foobarbaz' }
+    version(0.8, 'foobarbaz')
+    version(0.9, 'foobarbaz')
+    version(1.0, 'foobarbaz')
 
     depends_on("dyninst")
     depends_on("mpi")
diff --git a/var/spack/mock_packages/direct_mpich/package.py b/var/spack/mock_packages/direct_mpich/package.py
index d702e4481b7..2ced82521b3 100644
--- a/var/spack/mock_packages/direct_mpich/package.py
+++ b/var/spack/mock_packages/direct_mpich/package.py
@@ -28,7 +28,7 @@ class DirectMpich(Package):
     homepage = "http://www.example.com"
     url      = "http://www.example.com/direct_mpich-1.0.tar.gz"
 
-    versions = { 1.0 : 'foobarbaz' }
+    version('1.0', 'foobarbaz')
 
     depends_on('mpich')
 
diff --git a/var/spack/mock_packages/dyninst/package.py b/var/spack/mock_packages/dyninst/package.py
index d32c4b55043..7657e2c33f5 100644
--- a/var/spack/mock_packages/dyninst/package.py
+++ b/var/spack/mock_packages/dyninst/package.py
@@ -29,9 +29,8 @@ class Dyninst(Package):
     url      = "http://www.dyninst.org/sites/default/files/downloads/dyninst/8.1.2/DyninstAPI-8.1.2.tgz"
     list_url = "http://www.dyninst.org/downloads/dyninst-8.x"
 
-    versions = {
-        '8.1.2' : 'bf03b33375afa66fe0efa46ce3f4b17a',
-        '8.1.1' : '1f8743e3a5662b25ce64a7edf647e77d' }
+    version('8.1.2', 'bf03b33375afa66fe0efa46ce3f4b17a')
+    version('8.1.1', '1f8743e3a5662b25ce64a7edf647e77d')
 
     depends_on("libelf")
     depends_on("libdwarf")
diff --git a/var/spack/mock_packages/fake/package.py b/var/spack/mock_packages/fake/package.py
index 88bc6d86695..fb3c2bdd2e7 100644
--- a/var/spack/mock_packages/fake/package.py
+++ b/var/spack/mock_packages/fake/package.py
@@ -27,7 +27,8 @@
 class Fake(Package):
     homepage = "http://www.fake-spack-example.org"
     url      = "http://www.fake-spack-example.org/downloads/fake-1.0.tar.gz"
-    versions = { '1.0' : 'foobarbaz' }
+
+    version('1.0', 'foobarbaz')
 
     def install(self, spec, prefix):
         pass
diff --git a/var/spack/mock_packages/indirect_mpich/package.py b/var/spack/mock_packages/indirect_mpich/package.py
index a53cb9330c7..daf8b4b166e 100644
--- a/var/spack/mock_packages/indirect_mpich/package.py
+++ b/var/spack/mock_packages/indirect_mpich/package.py
@@ -32,7 +32,7 @@ class IndirectMpich(Package):
     homepage = "http://www.example.com"
     url      = "http://www.example.com/indirect_mpich-1.0.tar.gz"
 
-    versions = { 1.0 : 'foobarbaz' }
+    version(1.0, 'foobarbaz')
 
     depends_on('mpi')
     depends_on('direct_mpich')
diff --git a/var/spack/mock_packages/libdwarf/package.py b/var/spack/mock_packages/libdwarf/package.py
index 0f4d55fd884..0b8df04cfb2 100644
--- a/var/spack/mock_packages/libdwarf/package.py
+++ b/var/spack/mock_packages/libdwarf/package.py
@@ -33,10 +33,10 @@ class Libdwarf(Package):
     url      = "http://www.prevanders.net/libdwarf-20130729.tar.gz"
     list_url = homepage
 
-    versions = { 20130729 : "64b42692e947d5180e162e46c689dfbf",
-                 20130207 : 'foobarbaz',
-                 20111030 : 'foobarbaz',
-                 20070703 : 'foobarbaz' }
+    version(20130729, "64b42692e947d5180e162e46c689dfbf")
+    version(20130207, 'foobarbaz')
+    version(20111030, 'foobarbaz')
+    version(20070703, 'foobarbaz')
 
     depends_on("libelf")
 
diff --git a/var/spack/mock_packages/libelf/package.py b/var/spack/mock_packages/libelf/package.py
index 5ac07de4e3b..94c8f942cdb 100644
--- a/var/spack/mock_packages/libelf/package.py
+++ b/var/spack/mock_packages/libelf/package.py
@@ -28,9 +28,9 @@ class Libelf(Package):
     homepage = "http://www.mr511.de/software/english.html"
     url      = "http://www.mr511.de/software/libelf-0.8.13.tar.gz"
 
-    versions =   {'0.8.13' : '4136d7b4c04df68b686570afa26988ac',
-                  '0.8.12' : 'e21f8273d9f5f6d43a59878dc274fec7',
-                  '0.8.10' : '9db4d36c283d9790d8fa7df1f4d7b4d9' }
+    version('0.8.13', '4136d7b4c04df68b686570afa26988ac')
+    version('0.8.12', 'e21f8273d9f5f6d43a59878dc274fec7')
+    version('0.8.10', '9db4d36c283d9790d8fa7df1f4d7b4d9')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix,
diff --git a/var/spack/mock_packages/mpich/package.py b/var/spack/mock_packages/mpich/package.py
index 2a8e1cebe31..e86c1a68ac6 100644
--- a/var/spack/mock_packages/mpich/package.py
+++ b/var/spack/mock_packages/mpich/package.py
@@ -30,11 +30,11 @@ class Mpich(Package):
     list_url   = "http://www.mpich.org/static/downloads/"
     list_depth = 2
 
-    versions = { '3.0.4' : '9c5d5d4fe1e17dd12153f40bc5b6dbc0',
-                 '3.0.3' : 'foobarbaz',
-                 '3.0.2' : 'foobarbaz',
-                 '3.0.1' : 'foobarbaz',
-                 '3.0'   : 'foobarbaz' }
+    version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0')
+    version('3.0.3', 'foobarbaz')
+    version('3.0.2', 'foobarbaz')
+    version('3.0.1', 'foobarbaz')
+    version('3.0', 'foobarbaz')
 
     provides('mpi@:3', when='@3:')
     provides('mpi@:1', when='@1:')
diff --git a/var/spack/mock_packages/mpich2/package.py b/var/spack/mock_packages/mpich2/package.py
index 84dce4cccb7..827b94c8a4a 100644
--- a/var/spack/mock_packages/mpich2/package.py
+++ b/var/spack/mock_packages/mpich2/package.py
@@ -30,12 +30,12 @@ class Mpich2(Package):
     list_url   = "http://www.mpich.org/static/downloads/"
     list_depth = 2
 
-    versions = { '1.5' : '9c5d5d4fe1e17dd12153f40bc5b6dbc0',
-                 '1.4' : 'foobarbaz',
-                 '1.3' : 'foobarbaz',
-                 '1.2' : 'foobarbaz',
-                 '1.1' : 'foobarbaz',
-                 '1.0' : 'foobarbaz' }
+    version('1.5', '9c5d5d4fe1e17dd12153f40bc5b6dbc0')
+    version('1.4', 'foobarbaz')
+    version('1.3', 'foobarbaz')
+    version('1.2', 'foobarbaz')
+    version('1.1', 'foobarbaz')
+    version('1.0', 'foobarbaz')
 
     provides('mpi@:2.0')
     provides('mpi@:2.1', when='@1.1:')
diff --git a/var/spack/mock_packages/mpileaks/package.py b/var/spack/mock_packages/mpileaks/package.py
index c34d5991e64..c6be37bc13c 100644
--- a/var/spack/mock_packages/mpileaks/package.py
+++ b/var/spack/mock_packages/mpileaks/package.py
@@ -28,10 +28,10 @@ class Mpileaks(Package):
     homepage = "http://www.llnl.gov"
     url      = "http://www.llnl.gov/mpileaks-1.0.tar.gz"
 
-    versions = { 1.0 : 'foobarbaz',
-                 2.1 : 'foobarbaz',
-                 2.2 : 'foobarbaz',
-                 2.3 : 'foobarbaz' }
+    version(1.0, 'foobarbaz')
+    version(2.1, 'foobarbaz')
+    version(2.2, 'foobarbaz')
+    version(2.3, 'foobarbaz')
 
     depends_on("mpi")
     depends_on("callpath")
diff --git a/var/spack/mock_packages/trivial_install_test_package/package.py b/var/spack/mock_packages/trivial_install_test_package/package.py
index b665825b32d..c4db9f5f071 100644
--- a/var/spack/mock_packages/trivial_install_test_package/package.py
+++ b/var/spack/mock_packages/trivial_install_test_package/package.py
@@ -30,7 +30,7 @@ class TrivialInstallTestPackage(Package):
     homepage = "http://www.example.com/trivial_install"
     url      = "http://www.unit-test-should-replace-this-url/trivial_install-1.0.tar.gz"
 
-    versions = { '1.0' : 'foobarbaz' }
+    version('1.0', 'foobarbaz')
 
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix)
diff --git a/var/spack/mock_packages/zmpi/package.py b/var/spack/mock_packages/zmpi/package.py
index a86bd706bbf..8c6ceda6d3f 100644
--- a/var/spack/mock_packages/zmpi/package.py
+++ b/var/spack/mock_packages/zmpi/package.py
@@ -30,7 +30,7 @@ class Zmpi(Package):
     homepage = "http://www.spack-fake-zmpi.org"
     url      = "http://www.spack-fake-zmpi.org/downloads/zmpi-1.0.tar.gz"
 
-    versions = { '1.0' : 'foobarbaz' }
+    version('1.0', 'foobarbaz')
 
     provides('mpi@:10.0')
     depends_on('fake')
diff --git a/var/spack/packages/SAMRAI/package.py b/var/spack/packages/SAMRAI/package.py
index bb88ec32923..3dfb00b3917 100644
--- a/var/spack/packages/SAMRAI/package.py
+++ b/var/spack/packages/SAMRAI/package.py
@@ -11,17 +11,15 @@ class Samrai(Package):
     url      = "https://computation-rnd.llnl.gov/SAMRAI/download/SAMRAI-v3.7.3.tar.gz"
     list_url = homepage
 
-    versions = {
-      '3.7.3'      : '12d574eacadf8c9a70f1bb4cd1a69df6',
-      '3.7.2'      : 'f6a716f171c9fdbf3cb12f71fa6e2737',
-      '3.6.3-beta' : 'ef0510bf2893042daedaca434e5ec6ce',
-      '3.5.2-beta' : 'd072d9d681eeb9ada15ce91bea784274',
-      '3.5.0-beta' : '1ad18a319fc573e12e2b1fbb6f6b0a19',
-      '3.4.1-beta' : '00814cbee2cb76bf8302aff56bbb385b',
-      '3.3.3-beta' : '1db3241d3e1cab913dc310d736c34388',
-      '3.3.2-beta' : 'e598a085dab979498fcb6c110c4dd26c',
-      '2.4.4'      : '04fb048ed0efe7c531ac10c81cc5f6ac',
-    }
+    version('3.7.3',      '12d574eacadf8c9a70f1bb4cd1a69df6')
+    version('3.7.2',      'f6a716f171c9fdbf3cb12f71fa6e2737')
+    version('3.6.3-beta', 'ef0510bf2893042daedaca434e5ec6ce')
+    version('3.5.2-beta', 'd072d9d681eeb9ada15ce91bea784274')
+    version('3.5.0-beta', '1ad18a319fc573e12e2b1fbb6f6b0a19')
+    version('3.4.1-beta', '00814cbee2cb76bf8302aff56bbb385b')
+    version('3.3.3-beta', '1db3241d3e1cab913dc310d736c34388')
+    version('3.3.2-beta', 'e598a085dab979498fcb6c110c4dd26c')
+    version('2.4.4',      '04fb048ed0efe7c531ac10c81cc5f6ac')
 
     depends_on("mpi")
     depends_on("zlib")
diff --git a/var/spack/packages/boost/package.py b/var/spack/packages/boost/package.py
index 71c3058d795..d3231c3baab 100644
--- a/var/spack/packages/boost/package.py
+++ b/var/spack/packages/boost/package.py
@@ -14,32 +14,31 @@ class Boost(Package):
     list_url = "http://sourceforge.net/projects/boost/files/boost/"
     list_depth = 2
 
-    versions = {
-        '1.55.0' : 'd6eef4b4cacb2183f2bf265a5a03a354',
-        '1.54.0' : '15cb8c0803064faef0c4ddf5bc5ca279',
-        '1.53.0' : 'a00d22605d5dbcfb4c9936a9b35bc4c2',
-        '1.52.0' : '3a855e0f919107e0ca4de4d84ad3f750',
-        '1.51.0' : '4b6bd483b692fd138aef84ed2c8eb679',
-        '1.50.0' : '52dd00be775e689f55a987baebccc462',
-        '1.49.0' : '0d202cb811f934282dea64856a175698',
-        '1.48.0' : 'd1e9a7a7f532bb031a3c175d86688d95',
-        '1.47.0' : 'a2dc343f7bc7f83f8941e47ed4a18200',
-        '1.46.1' : '7375679575f4c8db605d426fc721d506',
-        '1.46.0' : '37b12f1702319b73876b0097982087e0',
-        '1.45.0' : 'd405c606354789d0426bc07bea617e58',
-        '1.44.0' : 'f02578f5218f217a9f20e9c30e119c6a',
-        '1.43.0' : 'dd49767bfb726b0c774f7db0cef91ed1',
-        '1.42.0' : '7bf3b4eb841b62ffb0ade2b82218ebe6',
-        '1.41.0' : '8bb65e133907db727a2a825c5400d0a6',
-        '1.40.0' : 'ec3875caeac8c52c7c129802a8483bd7',
-        '1.39.0' : 'a17281fd88c48e0d866e1a12deecbcc0',
-        '1.38.0' : '5eca2116d39d61382b8f8235915cb267',
-        '1.37.0' : '8d9f990bfb7e83769fa5f1d6f065bc92',
-        '1.36.0' : '328bfec66c312150e4c2a78dcecb504b',
-        '1.35.0' : 'dce952a7214e72d6597516bcac84048b',
-        '1.34.1' : '2d938467e8a448a2c9763e0a9f8ca7e5',
-        '1.34.0' : 'ed5b9291ffad776f8757a916e1726ad0'
-    }
+    version('1.55.0', 'd6eef4b4cacb2183f2bf265a5a03a354')
+    version('1.54.0', '15cb8c0803064faef0c4ddf5bc5ca279')
+    version('1.53.0', 'a00d22605d5dbcfb4c9936a9b35bc4c2')
+    version('1.52.0', '3a855e0f919107e0ca4de4d84ad3f750')
+    version('1.51.0', '4b6bd483b692fd138aef84ed2c8eb679')
+    version('1.50.0', '52dd00be775e689f55a987baebccc462')
+    version('1.49.0', '0d202cb811f934282dea64856a175698')
+    version('1.48.0', 'd1e9a7a7f532bb031a3c175d86688d95')
+    version('1.47.0', 'a2dc343f7bc7f83f8941e47ed4a18200')
+    version('1.46.1', '7375679575f4c8db605d426fc721d506')
+    version('1.46.0', '37b12f1702319b73876b0097982087e0')
+    version('1.45.0', 'd405c606354789d0426bc07bea617e58')
+    version('1.44.0', 'f02578f5218f217a9f20e9c30e119c6a')
+    version('1.43.0', 'dd49767bfb726b0c774f7db0cef91ed1')
+    version('1.42.0', '7bf3b4eb841b62ffb0ade2b82218ebe6')
+    version('1.41.0', '8bb65e133907db727a2a825c5400d0a6')
+    version('1.40.0', 'ec3875caeac8c52c7c129802a8483bd7')
+    version('1.39.0', 'a17281fd88c48e0d866e1a12deecbcc0')
+    version('1.38.0', '5eca2116d39d61382b8f8235915cb267')
+    version('1.37.0', '8d9f990bfb7e83769fa5f1d6f065bc92')
+    version('1.36.0', '328bfec66c312150e4c2a78dcecb504b')
+    version('1.35.0', 'dce952a7214e72d6597516bcac84048b')
+    version('1.34.1', '2d938467e8a448a2c9763e0a9f8ca7e5')
+    version('1.34.0', 'ed5b9291ffad776f8757a916e1726ad0')
+
 
     def url_for_version(self, version):
         """Handle Boost's weird URLs, which write the version two different ways."""
diff --git a/var/spack/packages/cmake/package.py b/var/spack/packages/cmake/package.py
index 70406610b6e..ca6553df84d 100644
--- a/var/spack/packages/cmake/package.py
+++ b/var/spack/packages/cmake/package.py
@@ -27,7 +27,8 @@
 class Cmake(Package):
     homepage  = 'https://www.cmake.org'
     url       = 'http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz'
-    versions  = { '2.8.10.2' : '097278785da7182ec0aea8769d06860c' }
+
+    version('2.8.10.2', '097278785da7182ec0aea8769d06860c')
 
     def install(self, spec, prefix):
         configure('--prefix='   + prefix,
diff --git a/var/spack/packages/dyninst/package.py b/var/spack/packages/dyninst/package.py
index 3f8696b6d8a..069237f7ffc 100644
--- a/var/spack/packages/dyninst/package.py
+++ b/var/spack/packages/dyninst/package.py
@@ -29,8 +29,8 @@ class Dyninst(Package):
     url      = "http://www.dyninst.org/sites/default/files/downloads/dyninst/8.1.2/DyninstAPI-8.1.2.tgz"
     list_url = "http://www.dyninst.org/downloads/dyninst-8.x"
 
-    versions = {'8.1.2' : 'bf03b33375afa66fe0efa46ce3f4b17a',
-                '8.1.1' : '1f8743e3a5662b25ce64a7edf647e77d' }
+    version('8.1.2', 'bf03b33375afa66fe0efa46ce3f4b17a')
+    version('8.1.1', '1f8743e3a5662b25ce64a7edf647e77d')
 
     depends_on("libelf")
     depends_on("libdwarf")
diff --git a/var/spack/packages/graphlib/package.py b/var/spack/packages/graphlib/package.py
index c959135147c..ddac0b2b66a 100644
--- a/var/spack/packages/graphlib/package.py
+++ b/var/spack/packages/graphlib/package.py
@@ -5,7 +5,7 @@ class Graphlib(Package):
     homepage = "http://https://github.com/lee218llnl/graphlib"
     url      = "https://github.com/lee218llnl/graphlib/archive/v2.0.0.tar.gz"
 
-    versions = { '2.0.0' : '43c6df84f1d38ba5a5dce0ae19371a70', }
+    version('2.0.0', '43c6df84f1d38ba5a5dce0ae19371a70')
 
     def install(self, spec, prefix):
         cmake(".", *std_cmake_args)
diff --git a/var/spack/packages/hdf5/package.py b/var/spack/packages/hdf5/package.py
index 7705676dba2..615c2a7fe4b 100644
--- a/var/spack/packages/hdf5/package.py
+++ b/var/spack/packages/hdf5/package.py
@@ -11,10 +11,10 @@ class Hdf5(Package):
     list_url = "http://www.hdfgroup.org/ftp/HDF5/releases"
     list_depth = 3
 
-    versions = { '1.8.13' : 'c03426e9e77d7766944654280b467289', }
+    version('1.8.13', 'c03426e9e77d7766944654280b467289')
 
     depends_on("mpi")
-    depends_on("zlib") 
+    depends_on("zlib")
 
     # TODO: currently hard-coded to use OpenMPI
     def install(self, spec, prefix):
diff --git a/var/spack/packages/launchmon/package.py b/var/spack/packages/launchmon/package.py
index 7f12f413088..b6773a85bc5 100644
--- a/var/spack/packages/launchmon/package.py
+++ b/var/spack/packages/launchmon/package.py
@@ -28,7 +28,7 @@ class Launchmon(Package):
     homepage = "http://sourceforge.net/projects/launchmon"
     url      = "http://downloads.sourceforge.net/project/launchmon/launchmon/1.0.1%20release/launchmon-1.0.1.tar.gz"
 
-    versions = { '1.0.1' : '2f12465803409fd07f91174a4389eb2b' }
+    version('1.0.1', '2f12465803409fd07f91174a4389eb2b')
 
     def install(self, spec, prefix):
         configure(
diff --git a/var/spack/packages/libdwarf/package.py b/var/spack/packages/libdwarf/package.py
index abd6d1f4a1d..c4d71ebc010 100644
--- a/var/spack/packages/libdwarf/package.py
+++ b/var/spack/packages/libdwarf/package.py
@@ -44,9 +44,9 @@ class Libdwarf(Package):
     url      = "http://www.prevanders.net/libdwarf-20130729.tar.gz"
     list_url = homepage
 
-    versions = { '20130729' : '4cc5e48693f7b93b7aa0261e63c0e21d',
-                 '20130207' : '64b42692e947d5180e162e46c689dfbf',
-                 '20130126' : 'ded74a5e90edb5a12aac3c29d260c5db' }
+    version('20130729', '4cc5e48693f7b93b7aa0261e63c0e21d')
+    version('20130207', '64b42692e947d5180e162e46c689dfbf')
+    version('20130126', 'ded74a5e90edb5a12aac3c29d260c5db')
 
     depends_on("libelf")
 
diff --git a/var/spack/packages/libelf/package.py b/var/spack/packages/libelf/package.py
index f663ba750d6..bf2fefabd50 100644
--- a/var/spack/packages/libelf/package.py
+++ b/var/spack/packages/libelf/package.py
@@ -33,8 +33,8 @@ class Libelf(Package):
     homepage = "http://www.mr511.de/software/english.html"
     url      = "http://www.mr511.de/software/libelf-0.8.13.tar.gz"
 
-    versions = { '0.8.13' : '4136d7b4c04df68b686570afa26988ac',
-                 '0.8.12' : 'e21f8273d9f5f6d43a59878dc274fec7', }
+    version('0.8.13', '4136d7b4c04df68b686570afa26988ac')
+    version('0.8.12', 'e21f8273d9f5f6d43a59878dc274fec7')
 
     def install(self, spec, prefix):
         configure("--prefix=" + prefix,
diff --git a/var/spack/packages/libevent/package.py b/var/spack/packages/libevent/package.py
index 9b45b532d7f..11b1083d672 100644
--- a/var/spack/packages/libevent/package.py
+++ b/var/spack/packages/libevent/package.py
@@ -11,18 +11,17 @@ class Libevent(Package):
     url      = "https://github.com/downloads/libevent/libevent/libevent-2.0.21-stable.tar.gz"
     list_url = "http://libevent.org/old-releases.html"
 
-    versions =   {
-      '2.0.21' : 'b2405cc9ebf264aa47ff615d9de527a2',
-      '2.0.20' : '94270cdee32c0cd0aa9f4ee6ede27e8e',
-      '2.0.19' : '91111579769f46055b0a438f5cc59572',
-      '2.0.18' : 'aa1ce9bc0dee7b8084f6855765f2c86a',
-      '2.0.17' : 'dad64aaaaff16b5fbec25160c06fee9a',
-      '2.0.16' : '899efcffccdb3d5111419df76e7dc8df',
-      '2.0.15' : '2643abe7ba242df15c08b2cc14ec8759',
-      '2.0.14' : 'cac0f379da35d3b98f83ac16fcfe1df4',
-      '2.0.13' : 'af786b4b3f790c9d3279792edf7867fc',
-      '2.0.12' : '42986228baf95e325778ed328a93e070',
-    }
+    version('2.0.21', 'b2405cc9ebf264aa47ff615d9de527a2')
+    version('2.0.20', '94270cdee32c0cd0aa9f4ee6ede27e8e')
+    version('2.0.19', '91111579769f46055b0a438f5cc59572')
+    version('2.0.18', 'aa1ce9bc0dee7b8084f6855765f2c86a')
+    version('2.0.17', 'dad64aaaaff16b5fbec25160c06fee9a')
+    version('2.0.16', '899efcffccdb3d5111419df76e7dc8df')
+    version('2.0.15', '2643abe7ba242df15c08b2cc14ec8759')
+    version('2.0.14', 'cac0f379da35d3b98f83ac16fcfe1df4')
+    version('2.0.13', 'af786b4b3f790c9d3279792edf7867fc')
+    version('2.0.12', '42986228baf95e325778ed328a93e070')
+
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
diff --git a/var/spack/packages/libunwind/package.py b/var/spack/packages/libunwind/package.py
index c93b5b2c987..aeadc85eb36 100644
--- a/var/spack/packages/libunwind/package.py
+++ b/var/spack/packages/libunwind/package.py
@@ -28,7 +28,7 @@ class Libunwind(Package):
     homepage = "http://www.nongnu.org/libunwind/"
     url      = "http://download.savannah.gnu.org/releases/libunwind/libunwind-1.1.tar.gz"
 
-    versions = { '1.1' : 'fb4ea2f6fbbe45bf032cd36e586883ce' }
+    version('1.1', 'fb4ea2f6fbbe45bf032cd36e586883ce')
 
     def install(self, spec, prefix):
         configure("--prefix=" + prefix)
diff --git a/var/spack/packages/mpich/package.py b/var/spack/packages/mpich/package.py
index 703614a5878..19a1efe9c36 100644
--- a/var/spack/packages/mpich/package.py
+++ b/var/spack/packages/mpich/package.py
@@ -32,7 +32,7 @@ class Mpich(Package):
     list_url   = "http://www.mpich.org/static/downloads/"
     list_depth = 2
 
-    versions = { '3.0.4' : '9c5d5d4fe1e17dd12153f40bc5b6dbc0' }
+    version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0')
 
     provides('mpi@:3', when='@3:')
     provides('mpi@:1', when='@1:')
diff --git a/var/spack/packages/mrnet/package.py b/var/spack/packages/mrnet/package.py
index 89eeaf1e714..6e9766f275c 100644
--- a/var/spack/packages/mrnet/package.py
+++ b/var/spack/packages/mrnet/package.py
@@ -5,8 +5,9 @@ class Mrnet(Package):
     homepage = "http://paradyn.org/mrnet"
     url      = "ftp://ftp.cs.wisc.edu/paradyn/mrnet/mrnet_4.0.0.tar.gz"
 
-    versions = { '4.0.0' : 'd00301c078cba57ef68613be32ceea2f', }
-    versions = { '4.1.0' : '5a248298b395b329e2371bf25366115c', }
+    version('4.0.0', 'd00301c078cba57ef68613be32ceea2f')
+    version('4.1.0', '5a248298b395b329e2371bf25366115c')
+
     parallel = False
 
     depends_on("boost")
diff --git a/var/spack/packages/mvapich2/package.py b/var/spack/packages/mvapich2/package.py
index f372679f49b..5b62835bf9a 100644
--- a/var/spack/packages/mvapich2/package.py
+++ b/var/spack/packages/mvapich2/package.py
@@ -2,11 +2,12 @@
 
 class Mvapich2(Package):
     """mvapich2 is an MPI implmenetation for infiniband networks."""
-
     homepage = "http://mvapich.cse.ohio-state.edu/"
-    url      = "http://mvapich.cse.ohio-state.edu/download/mvapich2/mv2/mvapich2-1.9.tgz"
 
-    versions = { '1.9' : '5dc58ed08fd3142c260b70fe297e127c', }
+    version('1.9', '5dc58ed08fd3142c260b70fe297e127c',
+            url="http://mvapich.cse.ohio-state.edu/download/mvapich2/mv2/mvapich2-1.9.tgz")
+    version('2.0', '9fbb68a4111a8b6338e476dc657388b4',
+            url='http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.0.tar.gz')
 
     provides('mpi@:1', when='@1.9:')
 
diff --git a/var/spack/packages/ncurses/package.py b/var/spack/packages/ncurses/package.py
index 221860374b2..4885caa628a 100644
--- a/var/spack/packages/ncurses/package.py
+++ b/var/spack/packages/ncurses/package.py
@@ -8,14 +8,12 @@ class Ncurses(Package):
     """
 
     homepage = "http://invisible-island.net/ncurses/ncurses.html"
-    url      = "http://invisible-island.net/datafiles/release/ncurses.tar.gz"
 
-    versions = { 'stable' : '8cb9c412e5f2d96bc6f459aa8c6282a1' }
+    version('5.9', '8cb9c412e5f2d96bc6f459aa8c6282a1',
+            url='http://invisible-island.net/datafiles/release/ncurses.tar.gz')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()
         make("install")
 
-    def url_for_version(self, version):
-        return "http://invisible-island.net/datafiles/release/ncurses.tar.gz"
diff --git a/var/spack/packages/openmpi/package.py b/var/spack/packages/openmpi/package.py
index 5ac231a33f2..0ce09bdd8db 100644
--- a/var/spack/packages/openmpi/package.py
+++ b/var/spack/packages/openmpi/package.py
@@ -12,7 +12,7 @@ class Openmpi(Package):
     homepage = "http://www.open-mpi.org"
     url      = "http://www.open-mpi.org/software/ompi/v1.6/downloads/openmpi-1.6.5.tar.bz2"
 
-    versions = { '1.6.5' : '03aed2a4aa4d0b27196962a2a65fc475', }
+    version('1.6.5', '03aed2a4aa4d0b27196962a2a65fc475')
 
     provides('mpi@:2')
 
diff --git a/var/spack/packages/parmetis/package.py b/var/spack/packages/parmetis/package.py
index 10a48503b2f..d8cd3373047 100644
--- a/var/spack/packages/parmetis/package.py
+++ b/var/spack/packages/parmetis/package.py
@@ -8,7 +8,7 @@ class Parmetis(Package):
     homepage = "http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview"
     url      = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz"
 
-    versions = { '4.0.3' : 'f69c479586bf6bb7aff6a9bc0c739628', }
+    version('4.0.3', 'f69c479586bf6bb7aff6a9bc0c739628')
 
     depends_on('mpi')
 
diff --git a/var/spack/packages/pmgr_collective/package.py b/var/spack/packages/pmgr_collective/package.py
index 0874e2d17b7..5d9b02acc31 100644
--- a/var/spack/packages/pmgr_collective/package.py
+++ b/var/spack/packages/pmgr_collective/package.py
@@ -30,7 +30,7 @@ class PmgrCollective(Package):
     homepage = "http://www.sourceforge.net/projects/pmgrcollective"
     url      = "http://downloads.sourceforge.net/project/pmgrcollective/pmgrcollective/PMGR_COLLECTIVE-1.0/pmgr_collective-1.0.tgz"
 
-    versions = { '1.0' : '0384d008774274cc3fc7b4d810dfd07e' }
+    version('1.0', '0384d008774274cc3fc7b4d810dfd07e')
 
     def install(self, spec, prefix):
         make('PREFIX="' + prefix + '"')
diff --git a/var/spack/packages/scr/package.py b/var/spack/packages/scr/package.py
index cb908e830e0..d480dba62fd 100644
--- a/var/spack/packages/scr/package.py
+++ b/var/spack/packages/scr/package.py
@@ -30,7 +30,7 @@ class Scr(Package):
 
     depends_on("mpi")
 
-    versions = { '1.1-7' : 'a5930e9ab27d1b7049447c2fd7734ebd' }
+    version('1.1-7', 'a5930e9ab27d1b7049447c2fd7734ebd')
 
     def install(self, spec, prefix):
         configure("--prefix=" + prefix,
diff --git a/var/spack/packages/spindle/package.py b/var/spack/packages/spindle/package.py
index 0d106221d85..bb0b74ab6fe 100644
--- a/var/spack/packages/spindle/package.py
+++ b/var/spack/packages/spindle/package.py
@@ -29,7 +29,7 @@ class Spindle(Package):
     url      = "https://github.com/hpc/Spindle/archive/v0.8.1.tar.gz"
     list_url = "https://github.com/hpc/Spindle/releases"
 
-    versions = {'0.8.1' : 'f11793a6b9d8df2cd231fccb2857d912' }
+    version('0.8.1', 'f11793a6b9d8df2cd231fccb2857d912')
 
     depends_on("launchmon")
 
diff --git a/var/spack/packages/stat/package.py b/var/spack/packages/stat/package.py
index 9f156d53e72..583ae48e82e 100644
--- a/var/spack/packages/stat/package.py
+++ b/var/spack/packages/stat/package.py
@@ -5,8 +5,8 @@ class Stat(Package):
     homepage = "http://paradyn.org/STAT/STAT.html"
     url      = "https://github.com/lee218llnl/stat/archive/v2.0.0.tar.gz"
 
-    versions = { '2.0.0' : 'c7494210b0ba26b577171b92838e1a9b', }
-    versions = { '2.1.0' : 'ece26beaf057aa9134d62adcdda1ba91', }
+    version('2.0.0', 'c7494210b0ba26b577171b92838e1a9b')
+    version('2.1.0', 'ece26beaf057aa9134d62adcdda1ba91')
 
     depends_on('libdwarf')
     depends_on('dyninst')
diff --git a/var/spack/packages/tau/package.py b/var/spack/packages/tau/package.py
index 62c467b572d..8d9dbe1759b 100644
--- a/var/spack/packages/tau/package.py
+++ b/var/spack/packages/tau/package.py
@@ -10,7 +10,8 @@ class Tau(Package):
     homepage = "http://www.cs.uoregon.edu/research/tau"
     url      = "http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/tau-2.23.1.tar.gz"
 
-    versions = { '2.23.1' : '6593b47ae1e7a838e632652f0426fe72', }
+    version('2.23.1', '6593b47ae1e7a838e632652f0426fe72')
+
 
     def install(self, spec, prefix):
         # TAU isn't happy with directories that have '@' in the path.  Sigh.
diff --git a/var/spack/packages/tmux/package.py b/var/spack/packages/tmux/package.py
index d4e3d9f8296..23d36db4275 100644
--- a/var/spack/packages/tmux/package.py
+++ b/var/spack/packages/tmux/package.py
@@ -10,7 +10,7 @@ class Tmux(Package):
     homepage = "http://tmux.sourceforge.net"
     url      = "http://downloads.sourceforge.net/project/tmux/tmux/tmux-1.9/tmux-1.9a.tar.gz"
 
-    versions = { '1.9a' : 'b07601711f96f1d260b390513b509a2d', }
+    version('1.9a', 'b07601711f96f1d260b390513b509a2d')
 
     depends_on('libevent')
     depends_on('ncurses')
diff --git a/var/spack/packages/vim/package.py b/var/spack/packages/vim/package.py
index 9398134b509..5c6d7cb56bc 100644
--- a/var/spack/packages/vim/package.py
+++ b/var/spack/packages/vim/package.py
@@ -13,19 +13,17 @@ class Vim(Package):
     url      = "ftp://ftp.vim.org/pub/vim/unix/vim-7.4.tar.bz2"
     list_url = "http://ftp.vim.org/pub/vim/unix/"
 
-    versions = {
-        '7.4' : '607e135c559be642f210094ad023dc65',
-        '7.3' : '5b9510a17074e2b37d8bb38ae09edbf2',
-        '7.2' : 'f0901284b338e448bfd79ccca0041254',
-        '7.1' : '44c6b4914f38d6f9aa959640b89da329',
-        '7.0' : '4ca69757678272f718b1041c810d82d8',
-        '6.4' : '774c14d93ce58674b3b2c880edd12d77',
-        '6.3' : '821fda8f14d674346b87e3ef9cb96389',
-        '6.2' : 'c49d360bbd069d00e2a57804f2a123d9',
-        '6.1.405' : 'd220ff58f2c72ed606e6d0297c2f2a7c',
-        '6.1' : '7fd0f915adc7c0dab89772884268b030',
-        '6.0' : '9d9ca84d489af6b3f54639dd97af3774',
-    }
+    version('7.4',     '607e135c559be642f210094ad023dc65')
+    version('7.3',     '5b9510a17074e2b37d8bb38ae09edbf2')
+    version('7.2',     'f0901284b338e448bfd79ccca0041254')
+    version('7.1',     '44c6b4914f38d6f9aa959640b89da329')
+    version('7.0',     '4ca69757678272f718b1041c810d82d8')
+    version('6.4',     '774c14d93ce58674b3b2c880edd12d77')
+    version('6.3',     '821fda8f14d674346b87e3ef9cb96389')
+    version('6.2',     'c49d360bbd069d00e2a57804f2a123d9')
+    version('6.1.405', 'd220ff58f2c72ed606e6d0297c2f2a7c')
+    version('6.1',     '7fd0f915adc7c0dab89772884268b030')
+    version('6.0',     '9d9ca84d489af6b3f54639dd97af3774')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
diff --git a/var/spack/packages/zlib/package.py b/var/spack/packages/zlib/package.py
index 608b27ddd39..2770f781ac3 100644
--- a/var/spack/packages/zlib/package.py
+++ b/var/spack/packages/zlib/package.py
@@ -9,7 +9,7 @@ class Zlib(Package):
     homepage = "http://zlib.net"
     url      = "http://zlib.net/zlib-1.2.8.tar.gz"
 
-    versions = { '1.2.8' : '44d667c142d7cda120332623eab69f40', }
+    version('1.2.8', '44d667c142d7cda120332623eab69f40')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)

From 5dffa2671124024bdb15d292751abd998702ab0d Mon Sep 17 00:00:00 2001
From: Luc Jaulmes <jaulmes1@llnl.gov>
Date: Fri, 20 Jun 2014 17:15:32 -0700
Subject: [PATCH 02/71] first try for ompss build script

---
 var/spack/packages/ompss/package.py | 41 +++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 var/spack/packages/ompss/package.py

diff --git a/var/spack/packages/ompss/package.py b/var/spack/packages/ompss/package.py
new file mode 100644
index 00000000000..32c9e13e297
--- /dev/null
+++ b/var/spack/packages/ompss/package.py
@@ -0,0 +1,41 @@
+from spack import *
+import os
+import glob
+import subprocess
+
+# working config lines for ompss 14.06 :
+#./mcxx-1.99.2/config.log:	$ ./configure --prefix=/usr/gapps/exmatex/ompss --with-nanox=/usr/gapps/exmatex/ompss --enable-ompss --with-mpi=/opt/mvapich2-intel-shmem-1.7 --enable-tl-openmp-profile --enable-tl-openmp-intel
+#./nanox-0.7/config.log:	$ ./configure --prefix=/usr/gapps/exmatex/ompss --with-mcc=/usr/gapps/exmatex/ompss/ --with-hwloc=/usr
+
+class Ompss(Package):
+    homepage = "http://pm.bsc.es/"
+    url      = "http://pm.bsc.es/sites/default/files/ftp/ompss/releases/ompss-14.06.tar.gz"
+    versions  = { '14.06' : '99be5dce74c0d7eea42636d26af47b4181ae2e11' }
+
+    # all dependencies are optional, really
+    depends_on("mpi")
+    #depends_on("openmp")
+    #depends_on("hwloc")
+
+    def install(self, spec, prefix):
+        if 'openmpi' in spec:
+            mpi = spec['openmpi']
+        elif 'mpich' in spec:
+            mpi = spec['mpich']
+        elif 'mvapich' in spec:
+            mpi = spec['mvapich']
+
+        os.chdir(glob.glob('./nanox-*').pop())
+        #configure("-prefix=" + prefix + " -with-mcc=" + prefix + " -with-hwloc=" + spec['hwloc'].prefix)
+        #configure("-prefix=" + prefix, "-with-mcc=" + prefix)
+        subprocess.check_call(["configure", "-prefix=" + prefix, "-with-mcc=" + prefix])
+        make()
+        make("install")
+
+        os.chdir(glob.glob('../mcxx-*').pop())
+        #configure("-prefix=" + prefix + " -with-nanox=" + prefix + " -enable-ompss -with-mpi=" + mpi.prefix)
+        #configure("-prefix=" + prefix, "-with-nanox=" + prefix, "-enable-ompss", "-with-mpi=" + mpi.prefix)
+        subprocess.check_call(['configure', "-prefix=" + prefix, "-with-nanox=" + prefix, "-enable-ompss", "-with-mpi=" + mpi.prefix])
+        make()
+        make("install")
+

From 5a4881c086111a07d93e0e7d5d4f25ba09bb56cc Mon Sep 17 00:00:00 2001
From: Luc Jaulmes <jaulmes1@llnl.gov>
Date: Fri, 20 Jun 2014 17:15:32 -0700
Subject: [PATCH 03/71] Adding Extrae and OmpSs with some of their
 dependencies, hwloc and PAPI. Extrae does not compile for latest versions of
 any MPI implementation.

---
 var/spack/packages/extrae/package.py   | 29 ++++++++++++++++++++++++++
 var/spack/packages/hwloc/package.py    | 15 +++++++++++++
 var/spack/packages/mvapich2/package.py |  2 --
 var/spack/packages/ompss/package.py    | 19 ++++++++---------
 var/spack/packages/papi/package.py     | 29 ++++++++++++++++++++++++++
 5 files changed, 82 insertions(+), 12 deletions(-)
 create mode 100644 var/spack/packages/extrae/package.py
 create mode 100644 var/spack/packages/hwloc/package.py
 create mode 100644 var/spack/packages/papi/package.py

diff --git a/var/spack/packages/extrae/package.py b/var/spack/packages/extrae/package.py
new file mode 100644
index 00000000000..a06f02d3df7
--- /dev/null
+++ b/var/spack/packages/extrae/package.py
@@ -0,0 +1,29 @@
+from spack import *
+
+class Extrae(Package):
+    homepage = "http://www.bsc.es/computer-sciences/extrae"
+    url      = "http://www.bsc.es/ssl/apps/performanceTools/files/extrae-2.5.1.tar.bz2"
+    versions = { '2.5.1' : '422376b9c68243bd36a8a73fa62de106', }
+
+    depends_on("mpi")
+    depends_on("dyninst")
+    depends_on("libunwind")
+    depends_on("boost")
+    depends_on("libdwarf")
+    depends_on("papi")
+
+    def install(self, spec, prefix):
+        if 'openmpi' in spec:
+            mpi = spec['openmpi']
+            if spec.satisfies('@2.5.1') and spec.satisfies('^openmpi@1.6.5'):
+                tty.error("Some headers conflict when using OpenMPI 1.6.5. Please use 1.6 instead.")
+        elif 'mpich' in spec:
+            mpi = spec['mpich']
+        elif 'mvapich2' in spec:
+            mpi = spec['mvapich2']
+
+        configure("--prefix=%s" % prefix, "--with-mpi=%s" % mpi.prefix, "--with-unwind=%s" % spec['libunwind'].prefix, "--with-dyninst=%s" % spec['dyninst'].prefix, "--with-boost=%s" % spec['boost'].prefix, "--with-dwarf=%s" % spec['libdwarf'].prefix, "--with-papi=%s" % spec['papi'].prefix, "--with-dyninst-headers=%s" % spec['dyninst'].prefix.include, "--with-dyninst-libs=%s" % spec['dyninst'].prefix.lib)
+
+        make()
+        make("install", parallel=False)
+
diff --git a/var/spack/packages/hwloc/package.py b/var/spack/packages/hwloc/package.py
new file mode 100644
index 00000000000..57c2ae2fa9a
--- /dev/null
+++ b/var/spack/packages/hwloc/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class Hwloc(Package):
+    """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently."""
+    homepage = "http://www.open-mpi.org/projects/hwloc/"
+    url      = "http://www.open-mpi.org/software/hwloc/v1.9/downloads/hwloc-1.9.tar.gz"
+
+    versions = { '1.9' : '1f9f9155682fe8946a97c08896109508', }
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+
+        make()
+        make("install")
+
diff --git a/var/spack/packages/mvapich2/package.py b/var/spack/packages/mvapich2/package.py
index 5b62835bf9a..0f0f849c512 100644
--- a/var/spack/packages/mvapich2/package.py
+++ b/var/spack/packages/mvapich2/package.py
@@ -11,8 +11,6 @@ class Mvapich2(Package):
 
     provides('mpi@:1', when='@1.9:')
 
-    patch('ad_lustre_rwcontig_open_source.patch', when='@1.9:')
-
     def install(self, spec, prefix):
         configure(
             "--prefix=" + prefix,
diff --git a/var/spack/packages/ompss/package.py b/var/spack/packages/ompss/package.py
index 32c9e13e297..66a126579ed 100644
--- a/var/spack/packages/ompss/package.py
+++ b/var/spack/packages/ompss/package.py
@@ -1,11 +1,10 @@
 from spack import *
 import os
 import glob
-import subprocess
 
 # working config lines for ompss 14.06 :
-#./mcxx-1.99.2/config.log:	$ ./configure --prefix=/usr/gapps/exmatex/ompss --with-nanox=/usr/gapps/exmatex/ompss --enable-ompss --with-mpi=/opt/mvapich2-intel-shmem-1.7 --enable-tl-openmp-profile --enable-tl-openmp-intel
-#./nanox-0.7/config.log:	$ ./configure --prefix=/usr/gapps/exmatex/ompss --with-mcc=/usr/gapps/exmatex/ompss/ --with-hwloc=/usr
+#./nanox-0.7/config.log:    $ ./configure --prefix=/usr/gapps/exmatex/ompss --with-mcc=/usr/gapps/exmatex/ompss/ --with-hwloc=/usr
+#./mcxx-1.99.2/config.log:    $ ./configure --prefix=/usr/gapps/exmatex/ompss --with-nanox=/usr/gapps/exmatex/ompss --enable-ompss --with-mpi=/opt/mvapich2-intel-shmem-1.7 --enable-tl-openmp-profile --enable-tl-openmp-intel
 
 class Ompss(Package):
     homepage = "http://pm.bsc.es/"
@@ -15,7 +14,7 @@ class Ompss(Package):
     # all dependencies are optional, really
     depends_on("mpi")
     #depends_on("openmp")
-    #depends_on("hwloc")
+    depends_on("hwloc")
 
     def install(self, spec, prefix):
         if 'openmpi' in spec:
@@ -25,17 +24,17 @@ def install(self, spec, prefix):
         elif 'mvapich' in spec:
             mpi = spec['mvapich']
 
+        openmp_options = ["--enable-tl-openmp-profile"]
+        if spec.satisfies('%intel'):
+            openmp_options.append( "--enable-tl-openmp-intel" )
+
         os.chdir(glob.glob('./nanox-*').pop())
-        #configure("-prefix=" + prefix + " -with-mcc=" + prefix + " -with-hwloc=" + spec['hwloc'].prefix)
-        #configure("-prefix=" + prefix, "-with-mcc=" + prefix)
-        subprocess.check_call(["configure", "-prefix=" + prefix, "-with-mcc=" + prefix])
+        configure("--prefix=%s" % prefix, "--with-mcc=%s" % prefix, "--with-hwloc=%s" % spec['hwloc'].prefix)
         make()
         make("install")
 
         os.chdir(glob.glob('../mcxx-*').pop())
-        #configure("-prefix=" + prefix + " -with-nanox=" + prefix + " -enable-ompss -with-mpi=" + mpi.prefix)
-        #configure("-prefix=" + prefix, "-with-nanox=" + prefix, "-enable-ompss", "-with-mpi=" + mpi.prefix)
-        subprocess.check_call(['configure', "-prefix=" + prefix, "-with-nanox=" + prefix, "-enable-ompss", "-with-mpi=" + mpi.prefix])
+        configure("--prefix=%s" % prefix, "--with-nanox=%s" % prefix, "--enable-ompss", "--with-mpi=%s" % mpi.prefix, *openmp_options)
         make()
         make("install")
 
diff --git a/var/spack/packages/papi/package.py b/var/spack/packages/papi/package.py
new file mode 100644
index 00000000000..15a621985b3
--- /dev/null
+++ b/var/spack/packages/papi/package.py
@@ -0,0 +1,29 @@
+from spack import *
+import os
+
+class Papi(Package):
+    """PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events.
+    In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack."""
+    homepage = "http://icl.cs.utk.edu/papi/index.html"
+    url      = "http://icl.cs.utk.edu/projects/papi/downloads/papi-5.3.0.tar.gz"
+
+    versions = { '5.3.0' : '367961dd0ab426e5ae367c2713924ffb', }
+
+    def install(self, spec, prefix):
+        os.chdir("src/")
+
+        configure_args=["--prefix=%s" % prefix]
+
+		# need to force consistency in the use of compilers
+        if spec.satisfies('%gcc'):
+            configure_args.append('CC=gcc')
+            configure_args.append('MPICH_CC=gcc')
+        if spec.satisfies('%intel'):
+            configure_args.append('CC=icc')
+            configure_args.append('MPICH_CC=icc')
+
+        configure(*configure_args)
+
+        make()
+        make("install")
+

From 853784d3829166f0d5b797dffcc2a8b63723e350 Mon Sep 17 00:00:00 2001
From: Luc Jaulmes <jaulmes1@llnl.gov>
Date: Tue, 24 Jun 2014 11:06:09 -0700
Subject: [PATCH 04/71] Added Paraver and dependencies, restricted Extrae to
 OpenMPI 1.6

---
 var/spack/packages/extrae/package.py     |  8 +++--
 var/spack/packages/ompss/package.py      |  1 +
 var/spack/packages/paraver/package.py    | 40 ++++++++++++++++++++++++
 var/spack/packages/wx/package.py         | 17 ++++++++++
 var/spack/packages/wxpropgrid/package.py | 17 ++++++++++
 5 files changed, 80 insertions(+), 3 deletions(-)
 create mode 100644 var/spack/packages/paraver/package.py
 create mode 100644 var/spack/packages/wx/package.py
 create mode 100644 var/spack/packages/wxpropgrid/package.py

diff --git a/var/spack/packages/extrae/package.py b/var/spack/packages/extrae/package.py
index a06f02d3df7..a4dae485b5e 100644
--- a/var/spack/packages/extrae/package.py
+++ b/var/spack/packages/extrae/package.py
@@ -1,11 +1,13 @@
 from spack import *
 
 class Extrae(Package):
+    """Extrae is the package devoted to generate tracefiles which can be analyzed later by Paraver. Extrae is a tool that uses different interposition mechanisms to inject probes into the target application so as to gather information regarding the application performance. The Extrae instrumentation package can instrument the MPI programin model, and the following parallel programming models either alone or in conjunction with MPI : OpenMP, CUDA, OpenCL, pthread, OmpSs"""
     homepage = "http://www.bsc.es/computer-sciences/extrae"
     url      = "http://www.bsc.es/ssl/apps/performanceTools/files/extrae-2.5.1.tar.bz2"
     versions = { '2.5.1' : '422376b9c68243bd36a8a73fa62de106', }
 
-    depends_on("mpi")
+    #depends_on("mpi")
+    depends_on("openmpi@:1.6")
     depends_on("dyninst")
     depends_on("libunwind")
     depends_on("boost")
@@ -15,8 +17,8 @@ class Extrae(Package):
     def install(self, spec, prefix):
         if 'openmpi' in spec:
             mpi = spec['openmpi']
-            if spec.satisfies('@2.5.1') and spec.satisfies('^openmpi@1.6.5'):
-                tty.error("Some headers conflict when using OpenMPI 1.6.5. Please use 1.6 instead.")
+            #if spec.satisfies('@2.5.1') and spec.satisfies('^openmpi@1.6.5'):
+            #    tty.error("Some headers conflict when using OpenMPI 1.6.5. Please use 1.6 instead.")
         elif 'mpich' in spec:
             mpi = spec['mpich']
         elif 'mvapich2' in spec:
diff --git a/var/spack/packages/ompss/package.py b/var/spack/packages/ompss/package.py
index 66a126579ed..4878a589bfb 100644
--- a/var/spack/packages/ompss/package.py
+++ b/var/spack/packages/ompss/package.py
@@ -7,6 +7,7 @@
 #./mcxx-1.99.2/config.log:    $ ./configure --prefix=/usr/gapps/exmatex/ompss --with-nanox=/usr/gapps/exmatex/ompss --enable-ompss --with-mpi=/opt/mvapich2-intel-shmem-1.7 --enable-tl-openmp-profile --enable-tl-openmp-intel
 
 class Ompss(Package):
+    """OmpSs is an effort to integrate features from the StarSs programming model developed by BSC into a single programming model. In particular, our objective is to extend OpenMP with new directives to support asynchronous parallelism and heterogeneity (devices like GPUs). However, it can also be understood as new directives extending other accelerator based APIs like CUDA or OpenCL. Our OmpSs environment is built on top of our Mercurium compiler and Nanos++ runtime system."""
     homepage = "http://pm.bsc.es/"
     url      = "http://pm.bsc.es/sites/default/files/ftp/ompss/releases/ompss-14.06.tar.gz"
     versions  = { '14.06' : '99be5dce74c0d7eea42636d26af47b4181ae2e11' }
diff --git a/var/spack/packages/paraver/package.py b/var/spack/packages/paraver/package.py
new file mode 100644
index 00000000000..d437adfa5dd
--- /dev/null
+++ b/var/spack/packages/paraver/package.py
@@ -0,0 +1,40 @@
+from spack import *
+import os
+
+class Paraver(Package):
+    """"A very powerful performance visualization and analysis tool based on
+     traces that can be used to analyse any information that is expressed on its input trace format.
+      Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae."""
+    homepage = "http://www.bsc.es/computer-sciences/performance-tools/paraver"
+    url      = "http://www.bsc.es/ssl/apps/performanceTools/files/paraver-sources-4.5.2.tar.gz"
+
+    versions = { '4.5.2' : 'ea463dd494519395c99ebae294edee17', }
+
+    depends_on("boost")
+    #depends_on("extrae")
+    depends_on("wx")
+    depends_on("wxpropgrid")
+
+    def install(self, spec, prefix):
+        os.chdir("ptools_common_files")
+        configure("--prefix=%s" % prefix)
+        make()
+        make("install")
+
+        os.chdir("../paraver-kernel")
+		#"--with-extrae=%s" % spec['extrae'].prefix, 
+        configure("--prefix=%s" % prefix, "--with-ptools-common-files=%s" % prefix, "--with-boost=%s" % spec['boost'].prefix, "--with-boost-serialization=boost_serialization")
+        make()
+        make("install")
+
+        os.chdir("../paraver-toolset")
+        configure("--prefix=%s" % prefix)
+        make()
+        make("install")
+
+        os.chdir("../wxparaver")
+		#"--with-extrae=%s" % spec['extrae'].prefix, 
+        configure("--prefix=%s" % prefix, "--with-paraver=%s" % prefix, "--with-boost=%s" % spec['boost'].prefix, "--with-boost-serialization=boost_serialization", "--with-wxdir=%s" % spec['wx'].prefix.bin)
+        make()
+        make("install")
+
diff --git a/var/spack/packages/wx/package.py b/var/spack/packages/wx/package.py
new file mode 100644
index 00000000000..de12f141b8d
--- /dev/null
+++ b/var/spack/packages/wx/package.py
@@ -0,0 +1,17 @@
+from spack import *
+
+class Wx(Package):
+    """wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI. It's also extensive, free, open-source and mature."""
+    homepage = "http://www.wxwidgets.org/"
+
+    url      = "https://sourceforge.net/projects/wxwindows/files/2.8.12/wxWidgets-2.8.12.tar.gz"
+    versions = { '2.8.12' : '2fa39da14bc06ea86fe902579fedc5b1', }
+#    url      = "https://sourceforge.net/projects/wxwindows/files/3.0.1/wxWidgets-3.0.1.tar.bz2"
+#    versions = { '3.0.1' : 'dad1f1cd9d4c370cbc22700dc492da31', }
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix, "--enable-unicode", "--disable-precomp-headers")
+
+        make(parallel=False)
+        make("install")
+
diff --git a/var/spack/packages/wxpropgrid/package.py b/var/spack/packages/wxpropgrid/package.py
new file mode 100644
index 00000000000..5cc244ca65b
--- /dev/null
+++ b/var/spack/packages/wxpropgrid/package.py
@@ -0,0 +1,17 @@
+from spack import *
+
+class Wxpropgrid(Package):
+    """wxPropertyGrid is a property sheet control for wxWidgets. In other words, it is a specialized two-column grid for editing properties such as strings, numbers, flagsets, string arrays, and colours."""
+    homepage = "http://wxpropgrid.sourceforge.net/"
+    url      = "http://prdownloads.sourceforge.net/wxpropgrid/wxpropgrid-1.4.15-src.tar.gz"
+
+    versions = { '1.4.15' : 'f44b5cd6fd60718bacfabbf7994f1e93', }
+
+    depends_on("wx")
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix, "--with-wxdir=%s" % spec['wx'].prefix.bin, "--enable-unicode")
+
+        make()
+        make("install")
+

From 5f3bcbfded0a4db4ec3979b82cfdb2c072f6c742 Mon Sep 17 00:00:00 2001
From: Luc Jaulmes <jaulmes1@llnl.gov>
Date: Tue, 29 Jul 2014 09:11:06 -0700
Subject: [PATCH 05/71] Addind missing dependency nanos->extrae necessary for
 traces

---
 var/spack/packages/ompss/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/packages/ompss/package.py b/var/spack/packages/ompss/package.py
index 4878a589bfb..8335ef0a801 100644
--- a/var/spack/packages/ompss/package.py
+++ b/var/spack/packages/ompss/package.py
@@ -16,6 +16,7 @@ class Ompss(Package):
     depends_on("mpi")
     #depends_on("openmp")
     depends_on("hwloc")
+    depends_on("extrae")
 
     def install(self, spec, prefix):
         if 'openmpi' in spec:
@@ -30,7 +31,7 @@ def install(self, spec, prefix):
             openmp_options.append( "--enable-tl-openmp-intel" )
 
         os.chdir(glob.glob('./nanox-*').pop())
-        configure("--prefix=%s" % prefix, "--with-mcc=%s" % prefix, "--with-hwloc=%s" % spec['hwloc'].prefix)
+        configure("--prefix=%s" % prefix, "--with-mcc=%s" % prefix, "--with-extrae=%s" % spec['extrae'].prefix, "--with-hwloc=%s" % spec['hwloc'].prefix)
         make()
         make("install")
 

From e011b767fafc1c7287db1cfd254266171e4e382f Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 31 Jul 2014 14:09:38 -0700
Subject: [PATCH 06/71] Converting Luc's packages to the new version format.

---
 var/spack/packages/extrae/package.py     | 11 +++++++++--
 var/spack/packages/hwloc/package.py      | 14 ++++++++++++--
 var/spack/packages/ompss/package.py      | 11 +++++++++--
 var/spack/packages/papi/package.py       | 12 +++++++++---
 var/spack/packages/paraver/package.py    | 13 +++++++------
 var/spack/packages/wx/package.py         | 17 ++++++++++++-----
 var/spack/packages/wxpropgrid/package.py |  7 +++++--
 7 files changed, 63 insertions(+), 22 deletions(-)

diff --git a/var/spack/packages/extrae/package.py b/var/spack/packages/extrae/package.py
index a4dae485b5e..3b842bc1ec6 100644
--- a/var/spack/packages/extrae/package.py
+++ b/var/spack/packages/extrae/package.py
@@ -1,10 +1,17 @@
 from spack import *
 
 class Extrae(Package):
-    """Extrae is the package devoted to generate tracefiles which can be analyzed later by Paraver. Extrae is a tool that uses different interposition mechanisms to inject probes into the target application so as to gather information regarding the application performance. The Extrae instrumentation package can instrument the MPI programin model, and the following parallel programming models either alone or in conjunction with MPI : OpenMP, CUDA, OpenCL, pthread, OmpSs"""
+    """Extrae is the package devoted to generate tracefiles which can
+       be analyzed later by Paraver. Extrae is a tool that uses
+       different interposition mechanisms to inject probes into the
+       target application so as to gather information regarding the
+       application performance. The Extrae instrumentation package can
+       instrument the MPI programin model, and the following parallel
+       programming models either alone or in conjunction with MPI :
+       OpenMP, CUDA, OpenCL, pthread, OmpSs"""
     homepage = "http://www.bsc.es/computer-sciences/extrae"
     url      = "http://www.bsc.es/ssl/apps/performanceTools/files/extrae-2.5.1.tar.bz2"
-    versions = { '2.5.1' : '422376b9c68243bd36a8a73fa62de106', }
+    version('2.5.1', '422376b9c68243bd36a8a73fa62de106')
 
     #depends_on("mpi")
     depends_on("openmpi@:1.6")
diff --git a/var/spack/packages/hwloc/package.py b/var/spack/packages/hwloc/package.py
index 57c2ae2fa9a..31a31f376a2 100644
--- a/var/spack/packages/hwloc/package.py
+++ b/var/spack/packages/hwloc/package.py
@@ -1,11 +1,21 @@
 from spack import *
 
 class Hwloc(Package):
-    """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently."""
+    """The Portable Hardware Locality (hwloc) software package
+       provides a portable abstraction (across OS, versions,
+       architectures, ...) of the hierarchical topology of modern
+       architectures, including NUMA memory nodes, sockets, shared
+       caches, cores and simultaneous multithreading. It also gathers
+       various system attributes such as cache and memory information
+       as well as the locality of I/O devices such as network
+       interfaces, InfiniBand HCAs or GPUs. It primarily aims at
+       helping applications with gathering information about modern
+       computing hardware so as to exploit it accordingly and
+       efficiently."""
     homepage = "http://www.open-mpi.org/projects/hwloc/"
     url      = "http://www.open-mpi.org/software/hwloc/v1.9/downloads/hwloc-1.9.tar.gz"
 
-    versions = { '1.9' : '1f9f9155682fe8946a97c08896109508', }
+    version('1.9', '1f9f9155682fe8946a97c08896109508')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
diff --git a/var/spack/packages/ompss/package.py b/var/spack/packages/ompss/package.py
index 8335ef0a801..544671de38f 100644
--- a/var/spack/packages/ompss/package.py
+++ b/var/spack/packages/ompss/package.py
@@ -7,10 +7,17 @@
 #./mcxx-1.99.2/config.log:    $ ./configure --prefix=/usr/gapps/exmatex/ompss --with-nanox=/usr/gapps/exmatex/ompss --enable-ompss --with-mpi=/opt/mvapich2-intel-shmem-1.7 --enable-tl-openmp-profile --enable-tl-openmp-intel
 
 class Ompss(Package):
-    """OmpSs is an effort to integrate features from the StarSs programming model developed by BSC into a single programming model. In particular, our objective is to extend OpenMP with new directives to support asynchronous parallelism and heterogeneity (devices like GPUs). However, it can also be understood as new directives extending other accelerator based APIs like CUDA or OpenCL. Our OmpSs environment is built on top of our Mercurium compiler and Nanos++ runtime system."""
+    """OmpSs is an effort to integrate features from the StarSs
+       programming model developed by BSC into a single programming
+       model. In particular, our objective is to extend OpenMP with
+       new directives to support asynchronous parallelism and
+       heterogeneity (devices like GPUs). However, it can also be
+       understood as new directives extending other accelerator based
+       APIs like CUDA or OpenCL. Our OmpSs environment is built on top
+       of our Mercurium compiler and Nanos++ runtime system."""
     homepage = "http://pm.bsc.es/"
     url      = "http://pm.bsc.es/sites/default/files/ftp/ompss/releases/ompss-14.06.tar.gz"
-    versions  = { '14.06' : '99be5dce74c0d7eea42636d26af47b4181ae2e11' }
+    version('14.06', '99be5dce74c0d7eea42636d26af47b4181ae2e11')
 
     # all dependencies are optional, really
     depends_on("mpi")
diff --git a/var/spack/packages/papi/package.py b/var/spack/packages/papi/package.py
index 15a621985b3..596f7114d60 100644
--- a/var/spack/packages/papi/package.py
+++ b/var/spack/packages/papi/package.py
@@ -2,12 +2,18 @@
 import os
 
 class Papi(Package):
-    """PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events.
-    In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack."""
+    """PAPI provides the tool designer and application engineer with a
+       consistent interface and methodology for use of the performance
+       counter hardware found in most major microprocessors. PAPI
+       enables software engineers to see, in near real time, the
+       relation between software performance and processor events.  In
+       addition Component PAPI provides access to a collection of
+       components that expose performance measurement opportunites
+       across the hardware and software stack."""
     homepage = "http://icl.cs.utk.edu/papi/index.html"
     url      = "http://icl.cs.utk.edu/projects/papi/downloads/papi-5.3.0.tar.gz"
 
-    versions = { '5.3.0' : '367961dd0ab426e5ae367c2713924ffb', }
+    version('5.3.0', '367961dd0ab426e5ae367c2713924ffb')
 
     def install(self, spec, prefix):
         os.chdir("src/")
diff --git a/var/spack/packages/paraver/package.py b/var/spack/packages/paraver/package.py
index d437adfa5dd..45bac95b283 100644
--- a/var/spack/packages/paraver/package.py
+++ b/var/spack/packages/paraver/package.py
@@ -2,13 +2,14 @@
 import os
 
 class Paraver(Package):
-    """"A very powerful performance visualization and analysis tool based on
-     traces that can be used to analyse any information that is expressed on its input trace format.
-      Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae."""
+    """"A very powerful performance visualization and analysis tool
+        based on traces that can be used to analyse any information that
+        is expressed on its input trace format.  Traces for parallel MPI,
+        OpenMP and other programs can be genereated with Extrae."""
     homepage = "http://www.bsc.es/computer-sciences/performance-tools/paraver"
     url      = "http://www.bsc.es/ssl/apps/performanceTools/files/paraver-sources-4.5.2.tar.gz"
 
-    versions = { '4.5.2' : 'ea463dd494519395c99ebae294edee17', }
+    version('4.5.2', 'ea463dd494519395c99ebae294edee17')
 
     depends_on("boost")
     #depends_on("extrae")
@@ -22,7 +23,7 @@ def install(self, spec, prefix):
         make("install")
 
         os.chdir("../paraver-kernel")
-		#"--with-extrae=%s" % spec['extrae'].prefix, 
+		#"--with-extrae=%s" % spec['extrae'].prefix,
         configure("--prefix=%s" % prefix, "--with-ptools-common-files=%s" % prefix, "--with-boost=%s" % spec['boost'].prefix, "--with-boost-serialization=boost_serialization")
         make()
         make("install")
@@ -33,7 +34,7 @@ def install(self, spec, prefix):
         make("install")
 
         os.chdir("../wxparaver")
-		#"--with-extrae=%s" % spec['extrae'].prefix, 
+		#"--with-extrae=%s" % spec['extrae'].prefix,
         configure("--prefix=%s" % prefix, "--with-paraver=%s" % prefix, "--with-boost=%s" % spec['boost'].prefix, "--with-boost-serialization=boost_serialization", "--with-wxdir=%s" % spec['wx'].prefix.bin)
         make()
         make("install")
diff --git a/var/spack/packages/wx/package.py b/var/spack/packages/wx/package.py
index de12f141b8d..1813a8c8a5a 100644
--- a/var/spack/packages/wx/package.py
+++ b/var/spack/packages/wx/package.py
@@ -1,13 +1,20 @@
 from spack import *
 
 class Wx(Package):
-    """wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI. It's also extensive, free, open-source and mature."""
+    """wxWidgets is a C++ library that lets developers create
+       applications for Windows, Mac OS X, Linux and other platforms
+       with a single code base. It has popular language bindings for
+       Python, Perl, Ruby and many other languages, and unlike other
+       cross-platform toolkits, wxWidgets gives applications a truly
+       native look and feel because it uses the platform's native API
+       rather than emulating the GUI. It's also extensive, free,
+       open-source and mature."""
     homepage = "http://www.wxwidgets.org/"
 
-    url      = "https://sourceforge.net/projects/wxwindows/files/2.8.12/wxWidgets-2.8.12.tar.gz"
-    versions = { '2.8.12' : '2fa39da14bc06ea86fe902579fedc5b1', }
-#    url      = "https://sourceforge.net/projects/wxwindows/files/3.0.1/wxWidgets-3.0.1.tar.bz2"
-#    versions = { '3.0.1' : 'dad1f1cd9d4c370cbc22700dc492da31', }
+    version('2.8.12', '2fa39da14bc06ea86fe902579fedc5b1',
+            url="https://sourceforge.net/projects/wxwindows/files/2.8.12/wxWidgets-2.8.12.tar.gz")
+    version('3.0.1', 'dad1f1cd9d4c370cbc22700dc492da31',
+            url="https://sourceforge.net/projects/wxwindows/files/3.0.1/wxWidgets-3.0.1.tar.bz2")
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix, "--enable-unicode", "--disable-precomp-headers")
diff --git a/var/spack/packages/wxpropgrid/package.py b/var/spack/packages/wxpropgrid/package.py
index 5cc244ca65b..790cead5178 100644
--- a/var/spack/packages/wxpropgrid/package.py
+++ b/var/spack/packages/wxpropgrid/package.py
@@ -1,11 +1,14 @@
 from spack import *
 
 class Wxpropgrid(Package):
-    """wxPropertyGrid is a property sheet control for wxWidgets. In other words, it is a specialized two-column grid for editing properties such as strings, numbers, flagsets, string arrays, and colours."""
+    """wxPropertyGrid is a property sheet control for wxWidgets. In
+       other words, it is a specialized two-column grid for editing
+       properties such as strings, numbers, flagsets, string arrays,
+       and colours."""
     homepage = "http://wxpropgrid.sourceforge.net/"
     url      = "http://prdownloads.sourceforge.net/wxpropgrid/wxpropgrid-1.4.15-src.tar.gz"
 
-    versions = { '1.4.15' : 'f44b5cd6fd60718bacfabbf7994f1e93', }
+    version('1.4.15', 'f44b5cd6fd60718bacfabbf7994f1e93')
 
     depends_on("wx")
 

From e377abc18c2cda1b967c2e663d1d9b56828ccfc0 Mon Sep 17 00:00:00 2001
From: David Boehme <boehme3@sierra648.llnl.gov>
Date: Thu, 31 Jul 2014 17:51:23 -0700
Subject: [PATCH 07/71] Add Score-P packages.

---
 var/spack/packages/cube/package.py     | 30 ++++++++++++++++++
 var/spack/packages/opari2/package.py   | 28 +++++++++++++++++
 var/spack/packages/otf2/package.py     | 38 +++++++++++++++++++++++
 var/spack/packages/scalasca/package.py | 43 ++++++++++++++++++++++++++
 var/spack/packages/scorep/package.py   | 41 ++++++++++++++++++++++++
 5 files changed, 180 insertions(+)
 create mode 100644 var/spack/packages/cube/package.py
 create mode 100644 var/spack/packages/opari2/package.py
 create mode 100644 var/spack/packages/otf2/package.py
 create mode 100644 var/spack/packages/scalasca/package.py
 create mode 100644 var/spack/packages/scorep/package.py

diff --git a/var/spack/packages/cube/package.py b/var/spack/packages/cube/package.py
new file mode 100644
index 00000000000..3a4f9542c66
--- /dev/null
+++ b/var/spack/packages/cube/package.py
@@ -0,0 +1,30 @@
+# FIXME: Add copyright statement
+#
+from spack import *
+
+class Cube(Package):
+    """Cube the profile viewer for Score-P and Scalasca profiles. It 
+       displays a multi-dimensional performance space consisting 
+       of the dimensions (i) performance metric, (ii) call path, 
+       and (iii) system resource."""
+
+    homepage = "http://www.scalasca.org/software/cube-4.x/download.html"
+    url      = "http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.3.tar.gz"
+
+    version('4.2.3', '8f95b9531f5a8f8134f279c2767c9b20')
+
+    def install(self, spec, prefix):
+        configure_args = ["--prefix=%s" % prefix, 
+                          "--without-paraver", 
+                          "--without-gui",
+                          "--enable-shared"]
+
+        if spec.satisfies('%gcc'):
+            configure_args.append('--with-nocross-compiler-suite=gcc')
+        if spec.satisfies('%intel'):
+            configure_args.append('--with-nocross-compiler-suite=intel')
+
+        configure(*configure_args)
+
+        make(parallel=False)
+        make("install", parallel=False)
diff --git a/var/spack/packages/opari2/package.py b/var/spack/packages/opari2/package.py
new file mode 100644
index 00000000000..b5711451956
--- /dev/null
+++ b/var/spack/packages/opari2/package.py
@@ -0,0 +1,28 @@
+# FIXME: Add copyright statement here 
+
+from spack import *
+
+class Opari2(Package):
+    """OPARI2 is a source-to-source instrumentation tool for OpenMP and 
+       hybrid codes. It surrounds OpenMP directives and runtime library 
+       calls with calls to the POMP2 measurement interface.
+       OPARI2 will provide you with a new initialization method that allows 
+       for multi-directory and parallel builds as well as the usage of 
+       pre-instrumented libraries. Furthermore, an efficient way of 
+       tracking parent-child relationships was added. Additionally, we 
+       extended OPARI2 to support instrumentation of OpenMP 3.0 
+       tied tasks. """
+
+    homepage = "http://www.vi-hps.org/projects/score-p"
+    url      = "http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.2.tar.gz"
+
+    version('1.1.2', '9a262c7ca05ff0ab5f7775ae96f3539e')
+
+    def install(self, spec, prefix):
+        # FIXME: Modify the configure line to suit your build system here.
+        configure("--prefix=%s" % prefix,
+                  "--enable-shared")
+
+        # FIXME: Add logic to build and install here
+        make()
+        make("install")
diff --git a/var/spack/packages/otf2/package.py b/var/spack/packages/otf2/package.py
new file mode 100644
index 00000000000..6e8c398d7d4
--- /dev/null
+++ b/var/spack/packages/otf2/package.py
@@ -0,0 +1,38 @@
+# FIXME: Add copyright
+
+from spack import *
+import os
+
+class Otf2(Package):
+    """The Open Trace Format 2 is a highly scalable, memory efficient event 
+       trace data format plus support library."""
+
+    homepage = "http://www.vi-hps.org/score-p"
+    url      = "http://www.vi-hps.org/upload/packages/otf2/otf2-1.4.tar.gz"
+
+    version('1.4',   'a23c42e936eb9209c4e08b61c3cf5092',
+            url="http://www.vi-hps.org/upload/packages/otf2/otf2-1.4.tar.gz")
+    version('1.3.1', 'd0ffc4e858455ace4f596f910e68c9f2',
+            url="http://www.vi-hps.org/upload/packages/otf2/otf2-1.3.1.tar.gz")
+    version('1.2.1', '8fb3e11fb7489896596ae2c7c83d7fc8',
+            url="http://www.vi-hps.org/upload/packages/otf2/otf2-1.2.1.tar.gz")
+
+    def install(self, spec, prefix):
+        # FIXME: Modify the configure line to suit your build system here.
+        cc = os.environ["SPACK_CC"]
+
+        configure_args=["--prefix=%s" % prefix,
+                        "--enable-shared"]
+
+        if spec.satisfies('%gcc'):
+            configure_args.append('--with-nocross-compiler-suite=gcc')
+        if spec.satisfies('%intel'):
+            configure_args.append('--with-nocross-compiler-suite=intel')
+        if spec.satisfies('%pgi'):
+            configure_args.append('--with-nocross-compiler-suite=pgi')
+            
+        configure(*configure_args)
+
+        # FIXME: Add logic to build and install here
+        make()
+        make("install")
diff --git a/var/spack/packages/scalasca/package.py b/var/spack/packages/scalasca/package.py
new file mode 100644
index 00000000000..b76d0a7df5c
--- /dev/null
+++ b/var/spack/packages/scalasca/package.py
@@ -0,0 +1,43 @@
+# FIXME: Add copyright
+
+from spack import *
+
+class Scalasca(Package):
+    """Scalasca is a software tool that supports the performance optimization
+       of parallel programs by measuring and analyzing their runtime behavior. 
+       The analysis identifies potential performance bottlenecks - in 
+       particular those concerning communication and synchronization - and 
+       offers guidance in exploring their causes."""
+
+    # FIXME: add a proper url for your package's homepage here.
+    homepage = "http://www.scalasca.org"
+    url      = "http://apps.fz-juelich.de/scalasca/releases/scalasca/2.1/dist/scalasca-2.1-rc2.tar.gz"
+
+    version('2.1-rc2', '1a95a39e5430539753e956a7524a756b')
+
+    depends_on("mpi")
+    depends_on("otf2@1.4")
+    depends_on("cube")
+
+    def install(self, spec, prefix):
+        configure_args = ["--prefix=%s" % prefix,
+                          "--with-otf2=%s" % spec['otf2'].prefix.bin,
+                          "--with-cube=%s" % spec['cube'].prefix.bin,
+                          "--enable-shared"]
+
+        if spec.satisfies('%gcc'):
+            configure_args.append('--with-nocross-compiler-suite=gcc')
+        if spec.satisfies('%intel'):
+            configure_args.append('--with-nocross-compiler-suite=intel')
+
+        configure(*configure_args)
+
+        make()
+        make("install")
+
+        # FIXME: Modify the configure line to suit your build system here.
+        configure("--prefix=%s" % prefix)
+
+        # FIXME: Add logic to build and install here
+        make()
+        make("install")
diff --git a/var/spack/packages/scorep/package.py b/var/spack/packages/scorep/package.py
new file mode 100644
index 00000000000..5c42cfdbf2a
--- /dev/null
+++ b/var/spack/packages/scorep/package.py
@@ -0,0 +1,41 @@
+# FIXME: Add copyright statement
+
+from spack import *
+
+class Scorep(Package):
+    """The Score-P measurement infrastructure is a highly scalable and 
+       easy-to-use tool suite for profiling, event tracing, and online 
+       analysis of HPC applications."""
+
+    # FIXME: add a proper url for your package's homepage here.
+    homepage = "http://www.vi-hps.org/projects/score-p"
+    url      = "http://www.vi-hps.org/upload/packages/scorep/scorep-1.2.3.tar.gz"
+
+    version('1.2.3', '4978084e7cbd05b94517aa8beaea0817')
+
+    depends_on("mpi")
+    depends_on("papi")
+    depends_on("otf2@1.2:1.2.1") 
+    depends_on("opari2")
+    depends_on("cube")
+
+    def install(self, spec, prefix):
+        configure_args = ["--prefix=%s" % prefix,
+                          "--with-otf2=%s" % spec['otf2'].prefix.bin,
+                          "--with-opari2=%s" % spec['opari2'].prefix.bin,
+                          "--with-cube=%s" % spec['cube'].prefix.bin,
+                          "--with-papi-header=%s" % spec['papi'].prefix.include,
+                          "--with-papi-lib=%s" % spec['papi'].prefix.lib,
+                          "--enable-shared"]
+
+        if spec.satisfies('%gcc'):
+            configure_args.append('--with-nocross-compiler-suite=gcc')
+        if spec.satisfies('%intel'):
+            configure_args.append('--with-nocross-compiler-suite=intel')
+        if spec.satisfies('%pgi'):
+            configure_args.append('--with-nocross-compiler-suite=pgi')
+
+        configure(*configure_args)
+
+        make()
+        make("install")

From 61e2cb56a440e0f1f3ddf84fdfeb048d8fb80443 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Fri, 1 Aug 2014 09:04:36 -0700
Subject: [PATCH 08/71] Got version 1.2.1 building, but 1.3 and onwards are
 different.

---
 var/spack/packages/otf2/package.py | 24 +++++++++++++++---------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/var/spack/packages/otf2/package.py b/var/spack/packages/otf2/package.py
index 6e8c398d7d4..7e284146233 100644
--- a/var/spack/packages/otf2/package.py
+++ b/var/spack/packages/otf2/package.py
@@ -4,7 +4,7 @@
 import os
 
 class Otf2(Package):
-    """The Open Trace Format 2 is a highly scalable, memory efficient event 
+    """The Open Trace Format 2 is a highly scalable, memory efficient event
        trace data format plus support library."""
 
     homepage = "http://www.vi-hps.org/score-p"
@@ -17,20 +17,26 @@ class Otf2(Package):
     version('1.2.1', '8fb3e11fb7489896596ae2c7c83d7fc8',
             url="http://www.vi-hps.org/upload/packages/otf2/otf2-1.2.1.tar.gz")
 
+
+    @when('@:1.2')
+    def version_specific_args(self, args):
+        return ["--with-platform=disabled"]
+
+    @when('@1.3:')
+    def version_specific_args(self, args):
+        # TODO: figure out what scorep's build does as of otf2 1.3
+        return []
+
+
     def install(self, spec, prefix):
         # FIXME: Modify the configure line to suit your build system here.
         cc = os.environ["SPACK_CC"]
 
         configure_args=["--prefix=%s" % prefix,
-                        "--enable-shared"]
+                        "--enable-shared"])
+
+        configure_args.extend(self.version_specific_args())
 
-        if spec.satisfies('%gcc'):
-            configure_args.append('--with-nocross-compiler-suite=gcc')
-        if spec.satisfies('%intel'):
-            configure_args.append('--with-nocross-compiler-suite=intel')
-        if spec.satisfies('%pgi'):
-            configure_args.append('--with-nocross-compiler-suite=pgi')
-            
         configure(*configure_args)
 
         # FIXME: Add logic to build and install here

From 513b5aecf1e34e775d98f12c41c9bd526a8504a5 Mon Sep 17 00:00:00 2001
From: David Boehme <boehme3@sierra324.llnl.gov>
Date: Fri, 1 Aug 2014 10:16:08 -0700
Subject: [PATCH 09/71] Improve compiler configuration in otf2 package

---
 var/spack/packages/otf2/package.py | 46 ++++++++++++++++++++++++------
 1 file changed, 38 insertions(+), 8 deletions(-)

diff --git a/var/spack/packages/otf2/package.py b/var/spack/packages/otf2/package.py
index 7e284146233..6f4ab997af1 100644
--- a/var/spack/packages/otf2/package.py
+++ b/var/spack/packages/otf2/package.py
@@ -1,6 +1,7 @@
 # FIXME: Add copyright
 
 from spack import *
+from contextlib import closing
 import os
 
 class Otf2(Package):
@@ -17,28 +18,57 @@ class Otf2(Package):
     version('1.2.1', '8fb3e11fb7489896596ae2c7c83d7fc8',
             url="http://www.vi-hps.org/upload/packages/otf2/otf2-1.2.1.tar.gz")
 
+    backend_user_provided = """\
+CC=cc
+CXX=c++
+F77=f77
+FC=f90
+CFLAGS=-fPIC
+CXXFLAGS=-fPIC
+"""
+    frontend_user_provided = """\
+CC_FOR_BUILD=cc
+CXX_FOR_BUILD=c++
+F77_FOR_BUILD=f70
+FC_FOR_BUILD=f90
+CFLAGS_FOR_BUILD=-fPIC
+CXXFLAGS_FOR_BUILD=-fPIC
+"""
+    mpi_user_provided = """\
+MPICC=cc
+MPICXX=c++
+MPIF77=f77
+MPIFC=f90
+MPI_CFLAGS=-fPIC
+MPI_CXXFLAGS=-fPIC
+"""
 
     @when('@:1.2')
-    def version_specific_args(self, args):
+    def version_specific_args(self):
         return ["--with-platform=disabled"]
 
     @when('@1.3:')
-    def version_specific_args(self, args):
+    def version_specific_args(self):
         # TODO: figure out what scorep's build does as of otf2 1.3
-        return []
-
+        return ["--with-custom-compilers"]
 
     def install(self, spec, prefix):
-        # FIXME: Modify the configure line to suit your build system here.
-        cc = os.environ["SPACK_CC"]
+        # Use a custom compiler configuration, otherwise the score-p
+        # build system messes with spack's compiler settings.
+        # Create these three files in the build directory
+        with closing(open("platform-backend-user-provided", "w")) as backend_file:
+            backend_file.write(self.backend_user_provided)
+        with closing(open("platform-frontend-user-provided", "w")) as frontend_file:
+            frontend_file.write(self.frontend_user_provided)
+        with closing(open("platform-mpi-user-provided", "w")) as mpi_file:
+            mpi_file.write(self.mpi_user_provided)            
 
         configure_args=["--prefix=%s" % prefix,
-                        "--enable-shared"])
+                        "--enable-shared"]
 
         configure_args.extend(self.version_specific_args())
 
         configure(*configure_args)
 
-        # FIXME: Add logic to build and install here
         make()
         make("install")

From d1de958daac3991bf673c4e5b10a0564a9a610d8 Mon Sep 17 00:00:00 2001
From: Matthew LeGendre <legendre1@llnl.gov>
Date: Fri, 1 Aug 2014 15:48:59 -0700
Subject: [PATCH 10/71] Add libmonitor to spack.  Still needs svn support for
 checkout

---
 var/spack/packages/libmonitor/package.py | 36 ++++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 var/spack/packages/libmonitor/package.py

diff --git a/var/spack/packages/libmonitor/package.py b/var/spack/packages/libmonitor/package.py
new file mode 100644
index 00000000000..ac84f2e9acb
--- /dev/null
+++ b/var/spack/packages/libmonitor/package.py
@@ -0,0 +1,36 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 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 Libmonitor(Package):
+    homepage = "http://hpctoolkit.org"
+    url      = "file:///g/g0/legendre/tools/oss/openspeedshop-release-2.1/SOURCES/libmonitor-20130218.tar.gz"
+
+    version('20130218', 'aa85c2c580e2dafb823cc47b09374279')
+
+    def install(self, spec, prefix):
+        configure("--prefix=" + prefix)
+        make()
+        make("install")

From b7fbc77babea727ee7620c8dbe48fd91ac953ff2 Mon Sep 17 00:00:00 2001
From: Matthew LeGendre <legendre1@llnl.gov>
Date: Fri, 1 Aug 2014 15:50:43 -0700
Subject: [PATCH 11/71] Add sqlite to spack

---
 var/spack/packages/sqlite/package.py | 35 ++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 var/spack/packages/sqlite/package.py

diff --git a/var/spack/packages/sqlite/package.py b/var/spack/packages/sqlite/package.py
new file mode 100644
index 00000000000..19013fb324d
--- /dev/null
+++ b/var/spack/packages/sqlite/package.py
@@ -0,0 +1,35 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 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 Sqlite(Package):
+    homepage = "www.sqlite.org"
+
+    version('3.8.5', '0544ef6d7afd8ca797935ccc2685a9ed', url='http://www.sqlite.org/2014/sqlite-autoconf-3080500.tar.gz')
+
+    def install(self, spec, prefix):
+        configure("--prefix=" + prefix)
+        make()
+        make("install")

From 557ae64d51f4b53eb7836b9b56b0a536836b3c55 Mon Sep 17 00:00:00 2001
From: David Boehme <boehme3@llnl.gov>
Date: Fri, 1 Aug 2014 16:39:29 -0700
Subject: [PATCH 12/71] Fix cube compiler configuration

---
 var/spack/packages/cube/package.py | 41 +++++++++++++++++++++++-------
 1 file changed, 32 insertions(+), 9 deletions(-)

diff --git a/var/spack/packages/cube/package.py b/var/spack/packages/cube/package.py
index 3a4f9542c66..16babb0b589 100644
--- a/var/spack/packages/cube/package.py
+++ b/var/spack/packages/cube/package.py
@@ -1,6 +1,7 @@
 # FIXME: Add copyright statement
 #
 from spack import *
+from contextlib import closing
 
 class Cube(Package):
     """Cube the profile viewer for Score-P and Scalasca profiles. It 
@@ -13,16 +14,38 @@ class Cube(Package):
 
     version('4.2.3', '8f95b9531f5a8f8134f279c2767c9b20')
 
-    def install(self, spec, prefix):
-        configure_args = ["--prefix=%s" % prefix, 
-                          "--without-paraver", 
-                          "--without-gui",
-                          "--enable-shared"]
+    version('4.3TP1', 'a2090fbc7b2ba394bd5c09ba971e237f', 
+            url = 'http://apps.fz-juelich.de/scalasca/releases/cube/4.3/dist/cube-4.3-TP1.tar.gz')
 
-        if spec.satisfies('%gcc'):
-            configure_args.append('--with-nocross-compiler-suite=gcc')
-        if spec.satisfies('%intel'):
-            configure_args.append('--with-nocross-compiler-suite=intel')
+    backend_user_provided = """\
+CC=cc
+CXX=c++
+F77=f77
+FC=f90
+#CFLAGS=-fPIC
+#CXXFLAGS=-fPIC
+"""
+    frontend_user_provided = """\
+CC_FOR_BUILD=cc
+CXX_FOR_BUILD=c++
+F77_FOR_BUILD=f70
+FC_FOR_BUILD=f90
+"""
+
+    def install(self, spec, prefix):
+        # Use a custom compiler configuration, otherwise the score-p
+        # build system messes with spack's compiler settings.
+        # Create these three files in the build directory
+
+        with closing(open("vendor/common/build-config/platforms/platform-backend-user-provided", "w")) as backend_file:
+            backend_file.write(self.backend_user_provided)
+        with closing(open("vendor/common/build-config/platforms/platform-frontend-user-provided", "w")) as frontend_file:
+            frontend_file.write(self.frontend_user_provided)
+
+        configure_args = ["--prefix=%s" % prefix,
+                          "--with-custom-compilers",
+                          "--without-paraver", 
+                          "--without-gui"]
 
         configure(*configure_args)
 

From d7a3c7e555bfd93fbf93ec55608d7fc6aa8052f8 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 3 Aug 2014 12:57:09 -0700
Subject: [PATCH 13/71] Fix up Matt's openss packages.

---
 lib/spack/spack/cmd/info.py              | 10 ++++++----
 var/spack/packages/libmonitor/package.py |  1 +
 var/spack/packages/sqlite/package.py     |  7 ++++++-
 3 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/lib/spack/spack/cmd/info.py b/lib/spack/spack/cmd/info.py
index 648dbf905a1..bb147b30f57 100644
--- a/lib/spack/spack/cmd/info.py
+++ b/lib/spack/spack/cmd/info.py
@@ -37,15 +37,17 @@ def info(parser, args):
     package = spack.db.get(args.name)
     print "Package:   ", package.name
     print "Homepage:  ", package.homepage
-    print "Download:  ", package.url
 
     print
     print "Safe versions:  "
 
-    if package.versions:
-        colify(reversed(sorted(package.versions)), indent=4)
+    if not package.versions:
+        print("None.")
     else:
-        print "None.  Use spack versions %s to get a list of downloadable versions." % package.name
+        maxlen = max(len(str(v)) for v in package.versions)
+        fmt = "%%-%ss" % maxlen
+        for v in reversed(sorted(package.versions)):
+            print "    " + (fmt % v) + "    " + package.url_for_version(v)
 
     print
     print "Dependencies:"
diff --git a/var/spack/packages/libmonitor/package.py b/var/spack/packages/libmonitor/package.py
index ac84f2e9acb..210712436a8 100644
--- a/var/spack/packages/libmonitor/package.py
+++ b/var/spack/packages/libmonitor/package.py
@@ -25,6 +25,7 @@
 from spack import *
 
 class Libmonitor(Package):
+    """Libmonitor is a library for process and thread control."""
     homepage = "http://hpctoolkit.org"
     url      = "file:///g/g0/legendre/tools/oss/openspeedshop-release-2.1/SOURCES/libmonitor-20130218.tar.gz"
 
diff --git a/var/spack/packages/sqlite/package.py b/var/spack/packages/sqlite/package.py
index 19013fb324d..734b0b6cb62 100644
--- a/var/spack/packages/sqlite/package.py
+++ b/var/spack/packages/sqlite/package.py
@@ -25,9 +25,14 @@
 from spack import *
 
 class Sqlite(Package):
+    """SQLite3 is an SQL database engine in a C library. Programs that
+       link the SQLite3 library can have SQL database access without
+       running a separate RDBMS process.
+    """
     homepage = "www.sqlite.org"
 
-    version('3.8.5', '0544ef6d7afd8ca797935ccc2685a9ed', url='http://www.sqlite.org/2014/sqlite-autoconf-3080500.tar.gz')
+    version('3.8.5', '0544ef6d7afd8ca797935ccc2685a9ed',
+            url='http://www.sqlite.org/2014/sqlite-autoconf-3080500.tar.gz')
 
     def install(self, spec, prefix):
         configure("--prefix=" + prefix)

From d0b179962b87470edbaf4e05e41e748bebe27a3d Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 4 Aug 2014 07:40:53 -0700
Subject: [PATCH 14/71] find and uninstall work when installed package is no
 longer in spack.

- Make switching between git branches easier.
- Make future removal of packages easier.
---
 lib/spack/spack/cmd/uninstall.py    | 11 ++++++-
 lib/spack/spack/directory_layout.py |  3 +-
 lib/spack/spack/package.py          |  9 +++---
 lib/spack/spack/spec.py             | 45 ++++++++++++++++++++++++-----
 4 files changed, 54 insertions(+), 14 deletions(-)

diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index 28a2f659ae0..73c98a203ba 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -28,6 +28,7 @@
 
 import spack
 import spack.cmd
+import spack.packages
 
 description="Remove an installed package"
 
@@ -68,7 +69,15 @@ def uninstall(parser, args):
         if len(matching_specs) == 0:
             tty.die("%s does not match any installed packages." % spec)
 
-        pkgs.extend(spack.db.get(s) for s in matching_specs)
+        for s in matching_specs:
+            try:
+                # should work if package is known to spack
+                pkgs.append(spack.db.get(s))
+
+            except spack.packages.UnknownPackageError, e:
+                # The package.py file has gone away -- but still want to uninstall.
+                spack.Package(s).do_uninstall(force=True)
+
 
     # Sort packages to be uninstalled by the number of installed dependents
     # This ensures we do things in the right order
diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index 28719521d2f..4fc00d536e7 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -155,7 +155,8 @@ def read_spec(self, path):
         """Read the contents of a file and parse them as a spec"""
         with closing(open(path)) as spec_file:
             string = spec_file.read().replace('\n', '')
-            return Spec(string)
+            # Specs from files are assumed normal and concrete
+            return Spec(string, concrete=True)
 
 
     def make_path_for_spec(self, spec):
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 90e77b5e826..8df658e6603 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -322,9 +322,6 @@ class SomePackage(Package):
 
 
     def __init__(self, spec):
-        # These attributes are required for all packages.
-        attr_required(self.__class__, 'homepage')
-
         # this determines how the package should be built.
         self.spec = spec
 
@@ -396,9 +393,13 @@ def stage(self):
             raise ValueError("Can only get a stage for a concrete package.")
 
         if self._stage is None:
+            if not self.url:
+                raise PackageVersionError(self.version)
+
             # TODO: move this logic into a mirror module.
             mirror_path = "%s/%s" % (self.name, "%s-%s.%s" % (
                 self.name, self.version, extension(self.url)))
+
             self._stage = Stage(
                 self.url, mirror_path=mirror_path, name=self.spec.short_spec)
         return self._stage
@@ -531,8 +532,6 @@ def nearest_url(version):
                     break
                 if self.versions[v].url:
                     url = self.versions[v].url
-            if not url:
-                raise PackageVersionError(v)
             return url
 
         if version in self.versions:
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index 1e2da10dcc6..45c3402617c 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -345,6 +345,17 @@ def __init__(self, spec_like, *dep_like, **kwargs):
         self.compiler = other.compiler
         self.dependencies = other.dependencies
 
+        # Specs are by default not assumed to be normal, but in some
+        # cases we've read them from a file want to assume normal.
+        # This allows us to manipulate specs that Spack doesn't have
+        # package.py files for.
+        self._normal = kwargs.get('normal', False)
+        self._concrete = kwargs.get('concrete', False)
+
+        # Specs cannot be concrete and non-normal.
+        if self._concrete:
+            self._normal = True
+
         # This allows users to construct a spec DAG with literals.
         # Note that given two specs a and b, Spec(a) copies a, but
         # Spec(a, b) will copy a but just add b as a dep.
@@ -432,11 +443,15 @@ def concrete(self):
            If any of the name, version, architecture, compiler, or depdenencies
            are ambiguous,then it is not concrete.
         """
-        return bool(not self.virtual
-                    and self.versions.concrete
-                    and self.architecture
-                    and self.compiler and self.compiler.concrete
-                    and self.dependencies.concrete)
+        if self._concrete:
+            return True
+
+        self._concrete = bool(not self.virtual
+                              and self.versions.concrete
+                              and self.architecture
+                              and self.compiler and self.compiler.concrete
+                              and self.dependencies.concrete)
+        return self._concrete
 
 
     def preorder_traversal(self, visited=None, d=0, **kwargs):
@@ -606,7 +621,7 @@ def _expand_virtual_packages(self):
 
             # If there are duplicate providers or duplicate provider deps, this
             # consolidates them and merges constraints.
-            self.normalize()
+            self.normalize(force=True)
 
 
     def concretize(self):
@@ -621,9 +636,13 @@ def concretize(self):
            with requirements of its pacakges.  See flatten() and normalize() for
            more details on this.
         """
+        if self._concrete:
+            return
+
         self.normalize()
         self._expand_virtual_packages()
         self._concretize_helper()
+        self._concrete = True
 
 
     def concretized(self):
@@ -754,7 +773,7 @@ def _normalize_helper(self, visited, spec_deps, provider_index):
             dependency._normalize_helper(visited, spec_deps, provider_index)
 
 
-    def normalize(self):
+    def normalize(self, **kwargs):
         """When specs are parsed, any dependencies specified are hanging off
            the root, and ONLY the ones that were explicitly provided are there.
            Normalization turns a partial flat spec into a DAG, where:
@@ -772,6 +791,9 @@ def normalize(self):
            TODO: normalize should probably implement some form of cycle detection,
            to ensure that the spec is actually a DAG.
         """
+        if self._normal and not kwargs.get('force', False):
+            return
+
         # Ensure first that all packages & compilers in the DAG exist.
         self.validate_names()
 
@@ -805,6 +827,9 @@ def normalize(self):
             raise InvalidDependencyException(
                 self.name + " does not depend on " + comma_or(extra))
 
+        # Mark the spec as normal once done.
+        self._normal = True
+
 
     def normalized(self):
         """Return a normalized copy of this spec without modifying this spec."""
@@ -1009,6 +1034,9 @@ def _dup(self, other, **kwargs):
         else:
             self.dependencies = DependencyMap()
 
+        self._normal = other._normal
+        self._concrete = other._concrete
+
 
     def copy(self, **kwargs):
         """Return a copy of this spec.
@@ -1261,6 +1289,9 @@ def spec(self):
         spec.dependents   = DependencyMap()
         spec.dependencies = DependencyMap()
 
+        spec._normal = False
+        spec._concrete = False
+
         # record this so that we know whether version is
         # unspecified or not.
         added_version = False

From 94c5c9667c786e05a635787e803d2cf7e22de73a Mon Sep 17 00:00:00 2001
From: David Beckingsale <davidbeckingsale@gmail.com>
Date: Thu, 31 Jul 2014 13:42:34 -0700
Subject: [PATCH 15/71] Added inital module support

---
 lib/spack/spack/__init__.py        |  1 +
 lib/spack/spack/cmd/load.py        | 50 +++++++++++++++
 lib/spack/spack/cmd/tclmodule.py   | 99 ++++++++++++++++++++++++++++++
 lib/spack/spack/cmd/unload.py      | 36 +++++++++++
 lib/spack/spack/hooks/tclmodule.py | 85 +++++++++++++++++++++++++
 share/spack/setup-env.bash         | 49 ++++++++++-----
 6 files changed, 304 insertions(+), 16 deletions(-)
 create mode 100644 lib/spack/spack/cmd/load.py
 create mode 100644 lib/spack/spack/cmd/tclmodule.py
 create mode 100644 lib/spack/spack/cmd/unload.py
 create mode 100644 lib/spack/spack/hooks/tclmodule.py

diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py
index 50fe453cfb7..bc24766510c 100644
--- a/lib/spack/spack/__init__.py
+++ b/lib/spack/spack/__init__.py
@@ -59,6 +59,7 @@
 install_path   = join_path(prefix, "opt")
 share_path     = join_path(prefix, "share", "spack")
 dotkit_path    = join_path(share_path, "dotkit")
+tclmodule_path    = join_path(share_path, "tclmodule")
 
 #
 # Set up the packages database.
diff --git a/lib/spack/spack/cmd/load.py b/lib/spack/spack/cmd/load.py
new file mode 100644
index 00000000000..1389740df15
--- /dev/null
+++ b/lib/spack/spack/cmd/load.py
@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by David Beckingsale, david@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 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 llnl.util.tty as tty
+import spack
+
+description ="Add package to environment using module."
+
+def setup_parser(subparser):
+    subparser.add_argument(
+        'spec', nargs=argparse.REMAINDER, help='Spec of package to add.')
+
+
+def print_help():
+    tty.msg("Spack module support is not initialized.",
+            "",
+            "To use module with Spack, you must first run the command",
+            "below, which you can copy and paste:",
+            "",
+            "For bash:",
+            "    . %s/setup-env.bash" % spack.share_path,
+            "",
+            "ksh/csh/tcsh shells are currently unsupported",
+            "")
+
+
+def load(parser, args):
+    print_help()
diff --git a/lib/spack/spack/cmd/tclmodule.py b/lib/spack/spack/cmd/tclmodule.py
new file mode 100644
index 00000000000..da5c4f95fc4
--- /dev/null
+++ b/lib/spack/spack/cmd/tclmodule.py
@@ -0,0 +1,99 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by David Beckingsale, david@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 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 sys
+import os
+import shutil
+import argparse
+
+import llnl.util.tty as tty
+from llnl.util.lang import partition_list
+from llnl.util.filesystem import mkdirp
+
+import spack.cmd
+import spack.hooks.tclmodule
+from spack.spec import Spec
+
+
+description ="Find modules for packages if they exist."
+
+def setup_parser(subparser):
+    subparser.add_argument(
+        '--refresh', action='store_true', help='Regenerate all modules')
+
+    subparser.add_argument(
+        'spec', nargs=argparse.REMAINDER, help='spec to find a module for.')
+
+
+def module_find(parser, args):
+    if not args.spec:
+        parser.parse_args(['tclmodule', '-h'])
+
+    spec = spack.cmd.parse_specs(args.spec)
+    if len(spec) > 1:
+        tty.die("You can only pass one spec.")
+    spec = spec[0]
+
+    if not spack.db.exists(spec.name):
+        tty.die("No such package: %s" % spec.name)
+
+    specs = [s for s in spack.db.installed_package_specs() if s.satisfies(spec)]
+
+    if len(specs) == 0:
+        tty.die("No installed packages match spec %s" % spec)
+
+    if len(specs) > 1:
+        tty.error("Multiple matches for spec %s.  Choose one:" % spec)
+        for s in specs:
+            sys.stderr.write(s.tree(color=True))
+        sys.exit(1)
+
+    match = specs[0]
+    if not os.path.isfile(spack.hooks.tclmodules.tclmodules_file(match.package)):
+        tty.die("No module is installed for package %s." % spec)
+
+    print match.format('$_$@$+$%@$=$#')
+
+
+def module_refresh(parser, args):
+    query_specs = spack.cmd.parse_specs(args.spec)
+
+    specs = spack.db.installed_package_specs()
+    if query_specs:
+        specs = [s for s in specs
+                 if any(s.satisfies(q) for q in query_specs)]
+    else:
+        shutil.rmtree(spack.module_path, ignore_errors=False)
+        mkdirp(spack.module_path)
+
+    for spec in specs:
+        spack.hooks.tclmodule.post_install(spec.package)
+
+
+
+def tclmodule(parser, args):
+    if args.refresh:
+        module_refresh(parser, args)
+    else:
+        module_find(parser, args)
diff --git a/lib/spack/spack/cmd/unload.py b/lib/spack/spack/cmd/unload.py
new file mode 100644
index 00000000000..df009c840b3
--- /dev/null
+++ b/lib/spack/spack/cmd/unload.py
@@ -0,0 +1,36 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by David Beckingsale, david@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 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.cmd.tclmodule
+
+description ="Remove package from environment using module."
+
+def setup_parser(subparser):
+    subparser.add_argument(
+        'spec', nargs=argparse.REMAINDER, help='Spec of package to remove.')
+
+
+def unload(parser, args):
+    spack.cmd.load.print_help()
diff --git a/lib/spack/spack/hooks/tclmodule.py b/lib/spack/spack/hooks/tclmodule.py
new file mode 100644
index 00000000000..7df41e267c7
--- /dev/null
+++ b/lib/spack/spack/hooks/tclmodule.py
@@ -0,0 +1,85 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by David Beckingsale, david@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 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 os
+import re
+import textwrap
+import shutil
+from contextlib import closing
+
+from llnl.util.filesystem import join_path, mkdirp
+
+import spack
+
+
+def module_file(pkg):
+    m_file_name = pkg.spec.format('$_$@$%@$+$=$#')
+    return join_path(spack.module_path, m_file_name)
+
+
+def post_install(pkg):
+    if not os.path.exists(spack.module_path):
+        mkdirp(spack.module_path)
+
+    alterations = []
+    for var, path in [
+        ('PATH', pkg.prefix.bin),
+        ('MANPATH', pkg.prefix.man),
+        ('MANPATH', pkg.prefix.share_man),
+        ('LD_LIBRARY_PATH', pkg.prefix.lib),
+        ('LD_LIBRARY_PATH', pkg.prefix.lib64)]:
+
+        if os.path.isdir(path):
+            alterations.append("prepend_path %s %s\n" % (var, path))
+
+    if not alterations:
+        return
+
+    alterations.append("prepend_path CMAKE_PREFIX_PATH %s\n" % pkg.prefix)
+
+    m_file = module_file(pkg)
+    with closing(open(m_file, 'w')) as m:
+        # Put everything in the spack category.
+        m.write('#%Module1.0\n')
+
+        m.write('module-whatis \"%s\"\n' % pkg.spec.format("$_ $@"))
+
+        # Recycle the description
+        if pkg.__doc__:
+            m.write('proc ModulesHelp { } {\n')
+            doc = re.sub(r'\s+', ' ', pkg.__doc__)
+            m.write("puts str \"%s\"\n" % doc)
+            m.write('}')
+
+
+        # Write alterations
+        for alter in alterations:
+            m.write(alter)
+
+
+def post_uninstall(pkg):
+    m_file = module_file(pkg)
+    if os.path.exists(m_file):
+        shutil.rmtree(m_file, ignore_errors=True)
+
diff --git a/share/spack/setup-env.bash b/share/spack/setup-env.bash
index e22a2591672..c23a5acab43 100755
--- a/share/spack/setup-env.bash
+++ b/share/spack/setup-env.bash
@@ -65,8 +65,38 @@ function spack {
     # Filter out use and unuse.  For any other commands, just run the
     # command.
     case $_spack_subcommand in
-        "use") ;;
-        "unuse") ;;
+        "use"|"unuse")
+            # Shift any other args for use off before parsing spec.
+            _spack_use_args=""
+            if [[ "$1" =~ ^- ]]; then
+                _spack_use_args="$1"; shift
+                _spack_spec="$@"
+            fi
+
+            # Here the user has run use or unuse with a spec.  Find a matching
+            # spec with a dotkit using spack dotkit, then use or unuse the
+            # result.  If spack dotkit comes back with an error, do nothing.
+            if _spack_full_spec=$(command spack dotkit $_spack_spec); then
+                $_spack_subcommand $_spack_use_args $_spack_full_spec
+            fi
+            return
+            ;;
+        "load"|"unload")
+            # Shift any other args for module off before parsing spec.
+            _spack_module_args=""
+            if [[ "$1" =~ ^- ]]; then
+                _spack_module_args="$1"; shift
+                _spack_spec="$@"
+            fi
+
+            # Here the user has run use or unuse with a spec.  Find a matching
+            # spec with a dotkit using spack dotkit, then use or unuse the
+            # result.  If spack dotkit comes back with an error, do nothing.
+            if _spack_full_spec=$(command spack tclmodule $_spack_spec); then
+                $_spack_subcommand $_spack_module_args $_spack_full_spec
+            fi
+            return
+            ;;
         *)
             command spack $_spack_subcommand "$@"
             return
@@ -79,19 +109,6 @@ function spack {
         return
     fi
 
-    # Shift any other args for use off before parsing spec.
-    _spack_use_args=""
-    if [[ "$1" =~ ^- ]]; then
-        _spack_use_args="$1"; shift
-        _spack_spec="$@"
-    fi
-
-    # Here the user has run use or unuse with a spec.  Find a matching
-    # spec with a dotkit using spack dotkit, then use or unuse the
-    # result.  If spack dotkit comes back with an error, do nothing.
-    if _spack_full_spec=$(command spack dotkit $_spack_spec); then
-        $_spack_subcommand $_spack_use_args $_spack_full_spec
-    fi
 }
 
 ########################################################################
@@ -128,5 +145,5 @@ _spack_share_dir="$(dirname ${BASH_SOURCE[0]})"
 _spack_prefix="$(dirname $(dirname $_spack_share_dir))"
 
 _spack_pathadd DK_NODE "$_spack_share_dir/dotkit"
+_spack_pathadd MODULEPATH "$_spack_share_dir/modules"
 _spack_pathadd PATH    "$_spack_prefix/bin"
-

From 57ddbd282aa58b084c1e2f3a2204a6fb9e7ac6e4 Mon Sep 17 00:00:00 2001
From: David Beckingsale <davidbeckingsale@gmail.com>
Date: Thu, 31 Jul 2014 14:56:45 -0700
Subject: [PATCH 16/71] Fixed up module support

---
 lib/spack/spack/__init__.py        |   2 +-
 lib/spack/spack/cmd/tclmodule.py   |   6 +-
 lib/spack/spack/hooks/tclmodule.py |  13 +--
 share/spack/setup-env.zsh          | 122 +++++++++++++++++++++++++++++
 4 files changed, 133 insertions(+), 10 deletions(-)
 create mode 100755 share/spack/setup-env.zsh

diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py
index bc24766510c..0b69ccde38f 100644
--- a/lib/spack/spack/__init__.py
+++ b/lib/spack/spack/__init__.py
@@ -59,7 +59,7 @@
 install_path   = join_path(prefix, "opt")
 share_path     = join_path(prefix, "share", "spack")
 dotkit_path    = join_path(share_path, "dotkit")
-tclmodule_path    = join_path(share_path, "tclmodule")
+tclmodule_path    = join_path(share_path, "modules")
 
 #
 # Set up the packages database.
diff --git a/lib/spack/spack/cmd/tclmodule.py b/lib/spack/spack/cmd/tclmodule.py
index da5c4f95fc4..270ee65b7b4 100644
--- a/lib/spack/spack/cmd/tclmodule.py
+++ b/lib/spack/spack/cmd/tclmodule.py
@@ -70,7 +70,7 @@ def module_find(parser, args):
         sys.exit(1)
 
     match = specs[0]
-    if not os.path.isfile(spack.hooks.tclmodules.tclmodules_file(match.package)):
+    if not os.path.isfile(spack.hooks.tclmodule.module_file(match.package)):
         tty.die("No module is installed for package %s." % spec)
 
     print match.format('$_$@$+$%@$=$#')
@@ -84,8 +84,8 @@ def module_refresh(parser, args):
         specs = [s for s in specs
                  if any(s.satisfies(q) for q in query_specs)]
     else:
-        shutil.rmtree(spack.module_path, ignore_errors=False)
-        mkdirp(spack.module_path)
+        shutil.rmtree(spack.tclmodule_path, ignore_errors=False)
+        mkdirp(spack.tclmodule_path)
 
     for spec in specs:
         spack.hooks.tclmodule.post_install(spec.package)
diff --git a/lib/spack/spack/hooks/tclmodule.py b/lib/spack/spack/hooks/tclmodule.py
index 7df41e267c7..d9b4a438319 100644
--- a/lib/spack/spack/hooks/tclmodule.py
+++ b/lib/spack/spack/hooks/tclmodule.py
@@ -35,7 +35,7 @@
 
 def module_file(pkg):
     m_file_name = pkg.spec.format('$_$@$%@$+$=$#')
-    return join_path(spack.module_path, m_file_name)
+    return join_path(spack.tclmodule_path, m_file_name)
 
 
 def post_install(pkg):
@@ -51,26 +51,27 @@ def post_install(pkg):
         ('LD_LIBRARY_PATH', pkg.prefix.lib64)]:
 
         if os.path.isdir(path):
-            alterations.append("prepend_path %s %s\n" % (var, path))
+            alterations.append("prepend-path %s \"%s\"\n" % (var, path))
 
     if not alterations:
         return
 
-    alterations.append("prepend_path CMAKE_PREFIX_PATH %s\n" % pkg.prefix)
+    alterations.append("prepend-path CMAKE_PREFIX_PATH \"%s\"\n" % pkg.prefix)
 
     m_file = module_file(pkg)
     with closing(open(m_file, 'w')) as m:
         # Put everything in the spack category.
         m.write('#%Module1.0\n')
 
-        m.write('module-whatis \"%s\"\n' % pkg.spec.format("$_ $@"))
+        m.write('module-whatis \"%s\"\n\n' % pkg.spec.format("$_ $@"))
 
         # Recycle the description
         if pkg.__doc__:
             m.write('proc ModulesHelp { } {\n')
             doc = re.sub(r'\s+', ' ', pkg.__doc__)
-            m.write("puts str \"%s\"\n" % doc)
-            m.write('}')
+            doc = re.sub(r'"', '\"', pkg.__doc__)
+            m.write("puts stderr \"%s\"\n" % doc)
+            m.write('}\n\n')
 
 
         # Write alterations
diff --git a/share/spack/setup-env.zsh b/share/spack/setup-env.zsh
new file mode 100755
index 00000000000..9aba92818d7
--- /dev/null
+++ b/share/spack/setup-env.zsh
@@ -0,0 +1,122 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by David Beckingsale, david@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+#
+#
+# This file is part of Spack and sets up the spack environment for zsh shells.
+# This includes dotkit and module support as well as putting spack
+# in your path.  Source it like this:
+#
+#    source /path/to/spack/share/spack/setup-env.zsh
+#
+#
+
+
+########################################################################
+# This is a wrapper around the spack command that forwards calls to
+# 'spack use' and 'spack unuse' to shell functions.  This in turn
+# allows them to be used to invoke dotkit functions.
+#
+# 'spack use' is smarter than just 'use' because it converts its
+# arguments into a unique spack spec that is then passed to dotkit
+# commands.  This allows the user to use packages without knowing all
+# their installation details.
+#
+# e.g., rather than requring a full spec for libelf, the user can type:
+#
+#     spack use libelf
+#
+# This will first find the available libelf dotkits and use a
+# matching one.  If there are two versions of libelf, the user would
+# need to be more specific, e.g.:
+#
+#     spack use libelf@0.8.13
+#
+# This is very similar to how regular spack commands work and it
+# avoids the need to come up with a user-friendly naming scheme for
+# spack dotfiles.
+########################################################################
+function spack {
+    _spack_subcommand=${1}; shift
+    _spack_spec="$@"
+
+    # Filter out use and unuse.  For any other commands, just run the
+    # command.
+    case ${_spack_subcommand} in
+        "use"|"unuse")
+            # Shift any other args for use off before parsing spec.
+            _spack_use_args=""
+            if [[ "$1" =~ ^- ]]; then
+                _spack_use_args="$1"; shift
+                _spack_spec="$@"
+            fi
+
+            # Here the user has run use or unuse with a spec.  Find a matching
+            # spec with a dotkit using spack dotkit, then use or unuse the
+            # result.  If spack dotkit comes back with an error, do nothing.
+            if _spack_full_spec=$(command spack dotkit $_spack_spec); then
+                $_spack_subcommand $_spack_use_args $_spack_full_spec
+            fi
+            return
+            ;;
+        "load"|"unload")
+            # Shift any other args for module off before parsing spec.
+            _spack_module_args=""
+            if [[ "$1" =~ ^- ]]; then
+                _spack_module_args="$1"; shift
+                _spack_spec="$@"
+            fi
+
+            # Here the user has run use or unuse with a spec.  Find a matching
+            # spec with a dotkit using spack dotkit, then use or unuse the
+            # result.  If spack dotkit comes back with an error, do nothing.
+            if _spack_full_spec=$(command spack tclmodule ${_spack_spec}); then
+                module ${_spack_subcommand} ${_spack_module_args} ${_spack_full_spec}
+            fi
+            return
+            ;;
+        *)
+            command spack $_spack_subcommand "$@"
+            return
+            ;;
+    esac
+
+    # If no args or -h, just run that command as well.
+    if [ -z "$1" -o "$1" = "-h" ]; then
+        command spack $_spack_subcommand -h
+        return
+    fi
+
+}
+
+#
+# Set up dotkit and path in the user environment
+#
+_spack_share_dir="$(dirname $0:A)"
+_spack_prefix="$(dirname $(dirname ${_spack_share_dir}))"
+
+export DK_NODE="$_spack_share_dir/dotkit:$DK_NODE"
+export MODULEPATH="$_spack_share_dir/modules:$MODULEPATH"
+export PATH="$_spack_prefix/bin:$PATH"

From 741084faf4194424a582bf9dd15580601f20fe9a Mon Sep 17 00:00:00 2001
From: Adam Moody <moody20@llnl.gov>
Date: Thu, 10 Jul 2014 16:55:38 -0700
Subject: [PATCH 17/71] add mvapich2 package to handle different compilers and
 variants

---
 var/spack/packages/mvapich2/package.py | 86 ++++++++++++++++++++++++--
 1 file changed, 82 insertions(+), 4 deletions(-)

diff --git a/var/spack/packages/mvapich2/package.py b/var/spack/packages/mvapich2/package.py
index 0f0f849c512..ca0b1287c1c 100644
--- a/var/spack/packages/mvapich2/package.py
+++ b/var/spack/packages/mvapich2/package.py
@@ -1,3 +1,4 @@
+import os
 from spack import *
 
 class Mvapich2(Package):
@@ -6,21 +7,98 @@ class Mvapich2(Package):
 
     version('1.9', '5dc58ed08fd3142c260b70fe297e127c',
             url="http://mvapich.cse.ohio-state.edu/download/mvapich2/mv2/mvapich2-1.9.tgz")
+    patch('ad_lustre_rwcontig_open_source.patch', when='@1.9')
+
     version('2.0', '9fbb68a4111a8b6338e476dc657388b4',
             url='http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.0.tar.gz')
 
-    provides('mpi@:1', when='@1.9:')
+    provides('mpi@:2.2', when='@1.9')    # MVAPICH2-1.9 supports MPI 2.2
+    provides('mpi@:3.0', when='@2.0')    # MVAPICH2-2.0 supports MPI 3.0
+
 
     def install(self, spec, prefix):
+        # we'll set different configure flags depending on our environment
+        configure_args = []
+
+        # TODO: The MPICH*_FLAGS have a different name for 1.9
+
+        if '+debug' in spec:
+            # set configure flags for debug build
+            configure_args.append("--disable-fast")
+            configure_args.append("--enable-g=dbg")
+            configure_args.append("--enable-error-checking=runtime")
+            configure_args.append("--enable-error-messages=all")
+            configure_args.append("--enable-nmpi-as-mpi")
+
+            if "%gnu" in spec:
+                # set variables for GNU compilers
+                os.environ['MPICHLIB_CFLAGS']   = "-g -O0"
+                os.environ['MPICHLIB_CXXFLAGS'] = "-g -O0"
+                os.environ['MPICHLIB_FFLAGS']   = "-g -O0 -fno-second-underscore"
+                os.environ['MPICHLIB_F90FLAGS'] = "-g -O0 -fno-second-underscore"
+            elif "%intel" in spec:
+                # set variables for Inel compilers
+                os.environ['MPICHLIB_CFLAGS']   = "-g -O0"
+                os.environ['MPICHLIB_CXXFLAGS'] = "-g -O0"
+                os.environ['MPICHLIB_FFLAGS']   = "-g -O0"
+                os.environ['MPICHLIB_F90FLAGS'] = "-g -O0"
+            elif "%pgi" in spec:
+                # set variables for PGI compilers
+                os.environ['MPICHLIB_CFLAGS']   = "-g -O0 -fPIC"
+                os.environ['MPICHLIB_CXXFLAGS'] = "-g -O0 -fPIC"
+                os.environ['MPICHLIB_FFLAGS']   = "-g -O0 -fPIC"
+                os.environ['MPICHLIB_F90FLAGS'] = "-g -O0 -fPIC"
+
+        else:
+            # set configure flags for normal optimizations
+            configure_args.append("--enable-fast=all")
+            configure_args.append("--enable-g=dbg")
+            configure_args.append("--enable-nmpi-as-mpi")
+
+            if "%gnu" in spec:
+                # set variables for what compilers
+                os.environ['MPICHLIB_CFLAGS']   = "-g -O2"
+                os.environ['MPICHLIB_CXXFLAGS'] = "-g -O2"
+                os.environ['MPICHLIB_FFLAGS']   = "-g -O2 -fno-second-underscore"
+                os.environ['MPICHLIB_F90FLAGS'] = "-g -O2 -fno-second-underscore"
+            elif "%intel" in spec:
+                # set variables for Inel compilers
+                os.environ['MPICHLIB_CFLAGS']   = "-g -O2"
+                os.environ['MPICHLIB_CXXFLAGS'] = "-g -O2"
+                os.environ['MPICHLIB_FFLAGS']   = "-g -O2"
+                os.environ['MPICHLIB_F90FLAGS'] = "-g -O2"
+            elif "%pgi" in spec:
+                # set variables for PGI compilers
+                os.environ['MPICHLIB_CFLAGS']   = "-g -O2 -fPIC"
+                os.environ['MPICHLIB_CXXFLAGS'] = "-g -O2 -fPIC"
+                os.environ['MPICHLIB_FFLAGS']   = "-g -O2 -fPIC"
+                os.environ['MPICHLIB_F90FLAGS'] = "-g -O2 -fPIC"
+
+        # determine network type by variant
+        if "+psm" in spec:
+            # throw this flag on QLogic systems to use PSM
+            configure_args.append("--with-device=ch3:psm")
+        else:
+            # throw this flag on IB systems
+            configure_args.append("--with-device=ch3:mrail", "--with-rdma=gen2")
+
+        # TODO: shared-memory build
+
+        # TODO: CUDA
+
+        # TODO: other file systems like panasis
+
         configure(
             "--prefix=" + prefix,
             "--enable-f77", "--enable-fc", "--enable-cxx",
-            "--enable-fast=all", "--enable-g=dbg", "--enable-nmpi-as-mpi",
             "--enable-shared", "--enable-sharedlibs=gcc",
             "--enable-debuginfo",
             "--with-pm=no", "--with-pmi=slurm",
-            "--with-device=ch3:psm",
             "--enable-romio", "--with-file-system=lustre+nfs+ufs",
-            "--disable-mpe", "--without-mpe")
+            "--disable-mpe", "--without-mpe",
+            "--disable-silent-rules",
+            *configure_args)
+
         make()
+
         make("install")

From 3dd8e561b90159de9ee57a7449298a4df09b3186 Mon Sep 17 00:00:00 2001
From: Adam Moody <moody20@llnl.gov>
Date: Thu, 31 Jul 2014 16:59:23 -0700
Subject: [PATCH 18/71] add lwgrp package

---
 var/spack/packages/lwgrp/package.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 var/spack/packages/lwgrp/package.py

diff --git a/var/spack/packages/lwgrp/package.py b/var/spack/packages/lwgrp/package.py
new file mode 100644
index 00000000000..d4054e195f1
--- /dev/null
+++ b/var/spack/packages/lwgrp/package.py
@@ -0,0 +1,17 @@
+import os
+from spack import *
+
+class Lwgrp(Package):
+    """Thie light-weight group library provides process group representations using O(log N) space and time."""
+
+    homepage = "https://github.com/hpc/lwgrp"
+    url      = "https://github.com/hpc/lwgrp/releases/download/v1.0.2/lwgrp-1.0.2.tar.gz"
+
+    versions = { '1.0.2' : 'ab7ba3bdd8534a651da5076f47f27d8a' }
+
+    depends_on('mpi')
+
+    def install(self, spec, prefix):
+        configure("--prefix=" + prefix)
+        make()
+        make("install")

From 6e7a7d127daa5bb2aafad6411f6c3cf4dbc2c640 Mon Sep 17 00:00:00 2001
From: Adam Moody <moody20@llnl.gov>
Date: Thu, 31 Jul 2014 18:56:38 -0700
Subject: [PATCH 19/71] adding dtcmp package

---
 var/spack/packages/dtcmp/package.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 var/spack/packages/dtcmp/package.py

diff --git a/var/spack/packages/dtcmp/package.py b/var/spack/packages/dtcmp/package.py
new file mode 100644
index 00000000000..400028bd6fc
--- /dev/null
+++ b/var/spack/packages/dtcmp/package.py
@@ -0,0 +1,20 @@
+import os
+from spack import *
+
+class Dtcmp(Package):
+    """The Datatype Comparison Library provides comparison operations and parallel sort algorithms for MPI applications."""
+
+    homepage = "https://github.com/hpc/dtcmp"
+    url      = "https://github.com/hpc/dtcmp/releases/download/v1.0.3/dtcmp-1.0.3.tar.gz"
+
+    versions = { '1.0.3' : 'cdd8ccf71e8ff67de2558594a7fcd317' }
+    #version('1.0.3', 'cdd8ccf71e8ff67de2558594a7fcd317')
+
+    depends_on('mpi')
+    depends_on('lwgrp')
+
+    def install(self, spec, prefix):
+        configure("--prefix=" + prefix,
+                  "--with-lwgrp=" + spec['lwgrp'].prefix)
+        make()
+        make("install")

From a32816c644450a8c419a2bbc19b020674dae547e Mon Sep 17 00:00:00 2001
From: Adam Moody <moody20@llnl.gov>
Date: Thu, 31 Jul 2014 21:31:20 -0700
Subject: [PATCH 20/71] cannot uninstall dtcmp because depends on dtcmp

---
 lib/spack/spack/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 8df658e6603..48074aaebbd 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -494,7 +494,7 @@ def installed_dependents(self):
            on this one."""
         dependents = []
         for spec in spack.db.installed_package_specs():
-            if self.spec != spec and self.spec in spec:
+            if self.name != spec.name and self.spec in spec:
                 dependents.append(spec)
         return dependents
 

From 712a2c374284420c7c6d0a53e43b32577ae9471f Mon Sep 17 00:00:00 2001
From: Adam Moody <moody20@llnl.gov>
Date: Fri, 1 Aug 2014 17:24:56 -0700
Subject: [PATCH 21/71] fileutils package

---
 var/spack/packages/fileutils/package.py | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 var/spack/packages/fileutils/package.py

diff --git a/var/spack/packages/fileutils/package.py b/var/spack/packages/fileutils/package.py
new file mode 100644
index 00000000000..8ddd3d060bc
--- /dev/null
+++ b/var/spack/packages/fileutils/package.py
@@ -0,0 +1,23 @@
+import os
+from spack import *
+
+class Fileutils(Package):
+    """FileUtils provides a suite of MPI-based tools to manage large files and datasets on parallel file systems."""
+
+    homepage = "https://github.com/hpc/fileutils"
+    url      = "https://github.com/hpc/fileutils/releases/download/v0.0.1-alpha.4/fileutils-0.0.1-alpha.4.tar.gz"
+
+    versions = { '0.0.1-alpha.4' : 'a01dbe5a2e03f3c70c7a98ec0a2554e1' }
+
+    force_url = True
+
+    depends_on('mpi')
+    depends_on('libcircle')
+    depends_on('libarchive')
+    depends_on('dtcmp')
+
+    def install(self, spec, prefix):
+        configure("--prefix=" + prefix,
+                  "--with-libdtcmp=" + spec['dtcmp'].prefix)
+        make()
+        make("install")

From a27e178ac27edf78c9c306a25091d6d1c36316e1 Mon Sep 17 00:00:00 2001
From: Adam Moody <moody20@llnl.gov>
Date: Fri, 1 Aug 2014 10:37:14 -0700
Subject: [PATCH 22/71] add libcircle package

---
 var/spack/packages/libcircle/package.py | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 var/spack/packages/libcircle/package.py

diff --git a/var/spack/packages/libcircle/package.py b/var/spack/packages/libcircle/package.py
new file mode 100644
index 00000000000..ae539969e7d
--- /dev/null
+++ b/var/spack/packages/libcircle/package.py
@@ -0,0 +1,22 @@
+import os
+from spack import *
+
+class Libcircle(Package):
+    """libcircle provides an efficient distributed queue on a cluster, using self-stabilizing work stealing."""
+
+    homepage = "https://github.com/hpc/libcircle"
+    #url      = "https://github.com/hpc/lwgrp/releases/download/v1.0.2/lwgrp-1.0.2.tar.gz"
+    url      = "https://github.com/adammoody/libcircle/releases/download/v0.2.1-rc.1/libcircle-0.2.1-rc.1.tar.gz"
+
+    versions = { '0.2.1-rc.1' : 'a10a14e76ac2ad7357a4b21b794e8e4e' }
+
+    # need this hack because the URL plus version string below confuses URL expansion
+    # at url_for_version() in lib/spack/package.py
+    force_url = True
+
+    depends_on('mpi')
+
+    def install(self, spec, prefix):
+        configure("--prefix=" + prefix)
+        make()
+        make("install")

From 3779c78c009fb7465bac25b4e59b5f710e3bd0da Mon Sep 17 00:00:00 2001
From: Adam Moody <moody20@llnl.gov>
Date: Thu, 31 Jul 2014 21:40:48 -0700
Subject: [PATCH 23/71] adding libarchive

---
 var/spack/packages/libarchive/package.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 var/spack/packages/libarchive/package.py

diff --git a/var/spack/packages/libarchive/package.py b/var/spack/packages/libarchive/package.py
new file mode 100644
index 00000000000..88c6ce45abc
--- /dev/null
+++ b/var/spack/packages/libarchive/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class Libarchive(Package):
+    """libarchive: C library and command-line tools for reading and writing tar, cpio, zip, ISO, and other archive formats."""
+    homepage = "http://www.libarchive.org"
+    url      = "http://www.libarchive.org/downloads/libarchive-3.1.2.tar.gz"
+
+    version('3.1.2', 'efad5a503f66329bb9d2f4308b5de98a')
+    version('3.1.1', '1f3d883daf7161a0065e42a15bbf168f')
+    version('3.1.0', '095a287bb1fd687ab50c85955692bf3a')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+        make()
+        make("install")

From cabfc374eb0fe546ea8377eb64f4415bbd11e3f8 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 3 Aug 2014 12:16:00 -0700
Subject: [PATCH 24/71] More descriptive error when package constructor fails.

- helps package_sanity test identify which package failed.
- encountered while upgrading versions in Adam's packages to the new format.
---
 lib/spack/spack/packages.py | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/lib/spack/spack/packages.py b/lib/spack/spack/packages.py
index 00834c95d54..4f9f606c899 100644
--- a/lib/spack/spack/packages.py
+++ b/lib/spack/spack/packages.py
@@ -69,7 +69,10 @@ def get(self, spec):
 
         if not spec in self.instances:
             package_class = self.get_class_for_package_name(spec.name)
-            self.instances[spec.name] = package_class(spec)
+            try:
+                self.instances[spec.name] = package_class(spec)
+            except Exception, e:
+                raise FailedConstructorError(spec.name, e)
 
         return self.instances[spec.name]
 
@@ -227,3 +230,12 @@ class UnknownPackageError(spack.error.SpackError):
     def __init__(self, name):
         super(UnknownPackageError, self).__init__("Package %s not found." % name)
         self.name = name
+
+
+class FailedConstructorError(spack.error.SpackError):
+    """Raised when a package's class constructor fails."""
+    def __init__(self, name, reason):
+        super(FailedConstructorError, self).__init__(
+            "Class constructor failed for package '%s'." % name,
+            str(reason))
+        self.name = name

From 782e45e5b1247f636f519c23de4cc54fe0cc21d1 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 3 Aug 2014 12:30:08 -0700
Subject: [PATCH 25/71] Fix up versions to match new version format, minor
 formatting.

---
 var/spack/packages/dtcmp/package.py      |  6 +++---
 var/spack/packages/fileutils/package.py  |  7 +++----
 var/spack/packages/libarchive/package.py |  3 ++-
 var/spack/packages/libcircle/package.py  | 10 +++-------
 var/spack/packages/lwgrp/package.py      |  5 +++--
 5 files changed, 14 insertions(+), 17 deletions(-)

diff --git a/var/spack/packages/dtcmp/package.py b/var/spack/packages/dtcmp/package.py
index 400028bd6fc..9d940583c12 100644
--- a/var/spack/packages/dtcmp/package.py
+++ b/var/spack/packages/dtcmp/package.py
@@ -2,13 +2,13 @@
 from spack import *
 
 class Dtcmp(Package):
-    """The Datatype Comparison Library provides comparison operations and parallel sort algorithms for MPI applications."""
+    """The Datatype Comparison Library provides comparison operations and
+       parallel sort algorithms for MPI applications."""
 
     homepage = "https://github.com/hpc/dtcmp"
     url      = "https://github.com/hpc/dtcmp/releases/download/v1.0.3/dtcmp-1.0.3.tar.gz"
 
-    versions = { '1.0.3' : 'cdd8ccf71e8ff67de2558594a7fcd317' }
-    #version('1.0.3', 'cdd8ccf71e8ff67de2558594a7fcd317')
+    version('1.0.3', 'cdd8ccf71e8ff67de2558594a7fcd317')
 
     depends_on('mpi')
     depends_on('lwgrp')
diff --git a/var/spack/packages/fileutils/package.py b/var/spack/packages/fileutils/package.py
index 8ddd3d060bc..449ed0c72e7 100644
--- a/var/spack/packages/fileutils/package.py
+++ b/var/spack/packages/fileutils/package.py
@@ -2,14 +2,13 @@
 from spack import *
 
 class Fileutils(Package):
-    """FileUtils provides a suite of MPI-based tools to manage large files and datasets on parallel file systems."""
+    """FileUtils provides a suite of MPI-based tools to manage large files
+       and datasets on parallel file systems."""
 
     homepage = "https://github.com/hpc/fileutils"
     url      = "https://github.com/hpc/fileutils/releases/download/v0.0.1-alpha.4/fileutils-0.0.1-alpha.4.tar.gz"
 
-    versions = { '0.0.1-alpha.4' : 'a01dbe5a2e03f3c70c7a98ec0a2554e1' }
-
-    force_url = True
+    version('0.0.1-alpha.4', 'a01dbe5a2e03f3c70c7a98ec0a2554e1')
 
     depends_on('mpi')
     depends_on('libcircle')
diff --git a/var/spack/packages/libarchive/package.py b/var/spack/packages/libarchive/package.py
index 88c6ce45abc..cbd4b89cd0e 100644
--- a/var/spack/packages/libarchive/package.py
+++ b/var/spack/packages/libarchive/package.py
@@ -1,7 +1,8 @@
 from spack import *
 
 class Libarchive(Package):
-    """libarchive: C library and command-line tools for reading and writing tar, cpio, zip, ISO, and other archive formats."""
+    """libarchive: C library and command-line tools for reading and
+       writing tar, cpio, zip, ISO, and other archive formats."""
     homepage = "http://www.libarchive.org"
     url      = "http://www.libarchive.org/downloads/libarchive-3.1.2.tar.gz"
 
diff --git a/var/spack/packages/libcircle/package.py b/var/spack/packages/libcircle/package.py
index ae539969e7d..e398125328a 100644
--- a/var/spack/packages/libcircle/package.py
+++ b/var/spack/packages/libcircle/package.py
@@ -2,17 +2,13 @@
 from spack import *
 
 class Libcircle(Package):
-    """libcircle provides an efficient distributed queue on a cluster, using self-stabilizing work stealing."""
+    """libcircle provides an efficient distributed queue on a cluster,
+       using self-stabilizing work stealing."""
 
     homepage = "https://github.com/hpc/libcircle"
-    #url      = "https://github.com/hpc/lwgrp/releases/download/v1.0.2/lwgrp-1.0.2.tar.gz"
     url      = "https://github.com/adammoody/libcircle/releases/download/v0.2.1-rc.1/libcircle-0.2.1-rc.1.tar.gz"
 
-    versions = { '0.2.1-rc.1' : 'a10a14e76ac2ad7357a4b21b794e8e4e' }
-
-    # need this hack because the URL plus version string below confuses URL expansion
-    # at url_for_version() in lib/spack/package.py
-    force_url = True
+    version('0.2.1-rc.1', 'a10a14e76ac2ad7357a4b21b794e8e4e')
 
     depends_on('mpi')
 
diff --git a/var/spack/packages/lwgrp/package.py b/var/spack/packages/lwgrp/package.py
index d4054e195f1..5963382b925 100644
--- a/var/spack/packages/lwgrp/package.py
+++ b/var/spack/packages/lwgrp/package.py
@@ -2,12 +2,13 @@
 from spack import *
 
 class Lwgrp(Package):
-    """Thie light-weight group library provides process group representations using O(log N) space and time."""
+    """Thie light-weight group library provides process group
+       representations using O(log N) space and time."""
 
     homepage = "https://github.com/hpc/lwgrp"
     url      = "https://github.com/hpc/lwgrp/releases/download/v1.0.2/lwgrp-1.0.2.tar.gz"
 
-    versions = { '1.0.2' : 'ab7ba3bdd8534a651da5076f47f27d8a' }
+    version('1.0.2', 'ab7ba3bdd8534a651da5076f47f27d8a')
 
     depends_on('mpi')
 

From 8738a3a88c48fd9ed2a9c6182e71e94e6e2d5c3f Mon Sep 17 00:00:00 2001
From: David Beckingsale <davidbeckingsale@gmail.com>
Date: Thu, 31 Jul 2014 15:37:35 -0700
Subject: [PATCH 26/71] Added LLVM package

---
 var/spack/packages/llvm/package.py | 48 ++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 var/spack/packages/llvm/package.py

diff --git a/var/spack/packages/llvm/package.py b/var/spack/packages/llvm/package.py
new file mode 100644
index 00000000000..dab10f77d37
--- /dev/null
+++ b/var/spack/packages/llvm/package.py
@@ -0,0 +1,48 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by David Beckingsale, david@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 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 Llvm(Package):
+    """The LLVM Project is a collection of modular and reusable compiler and
+       toolchain technologies. Despite its name, LLVM has little to do with
+       traditional virtual machines, though it does provide helpful libraries
+       that can be used to build them. The name "LLVM" itself is not an acronym;
+       it is the full name of the project.
+    """
+    homepage = "http://llvm.org/"
+    url      = "http://llvm.org/releases/3.4.2/llvm-3.4.2.src.tar.gz"
+
+    version('3.4.2', 'a20669f75967440de949ac3b1bad439c')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix,
+            "--enable-optimized",
+            "--enable-debug-runtime",
+            "--enable-debug-symbols",
+            "--disable-assertions",
+            "REQUIRES_RTTI=1")
+
+        make()
+        make("install")

From c55041e9d47cba97fc461c088c4b935b3355e340 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Fri, 1 Aug 2014 08:33:00 -0700
Subject: [PATCH 27/71] Partial commit of more packages.

---
 README.md                                     | 18 +++++-
 lib/spack/llnl/util/filesystem.py             | 21 ++++---
 lib/spack/spack/build_environment.py          |  5 +-
 lib/spack/spack/cmd/create.py                 | 30 +++++-----
 lib/spack/spack/package.py                    |  2 +-
 lib/spack/spack/util/executable.py            |  2 +-
 var/spack/packages/clang/package.py           | 47 +++++++++++++++
 .../packages/llvm-compiler-rt/package.py      | 57 +++++++++++++++++++
 var/spack/packages/llvm-lld/package.py        | 46 +++++++++++++++
 var/spack/packages/llvm/package.py            | 18 +++---
 10 files changed, 210 insertions(+), 36 deletions(-)
 create mode 100644 var/spack/packages/clang/package.py
 create mode 100644 var/spack/packages/llvm-compiler-rt/package.py
 create mode 100644 var/spack/packages/llvm-lld/package.py

diff --git a/README.md b/README.md
index c883cf44b43..11d505a7799 100644
--- a/README.md
+++ b/README.md
@@ -35,4 +35,20 @@ for Spack is also available.
 Authors
 ----------------
 Spack was written by Todd Gamblin, tgamblin@llnl.gov.
-LLNL-CODE-647188
+
+Significant contributions were also made by the following awesome
+people:
+
+  * David Beckingsale
+  * David Boehme
+  * Luc Jaulmes
+  * Matt Legendre
+  * Greg Lee
+  * Adam Moody
+
+Release
+----------------
+Spack is released under an LGPL license.  For more details see the
+LICENSE file.
+
+``LLNL-CODE-647188``
diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index 11c3dee6049..3782aefcced 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -124,8 +124,19 @@ def expand_user(path):
     return path.replace('%u', username)
 
 
+def mkdirp(*paths):
+    for path in paths:
+        if not os.path.exists(path):
+            os.makedirs(path)
+        elif not os.path.isdir(path):
+            raise OSError(errno.EEXIST, "File alredy exists", path)
+
+
 @contextmanager
-def working_dir(dirname):
+def working_dir(dirname, **kwargs):
+    if kwargs.get('create', False):
+        mkdirp(dirname)
+
     orig_dir = os.getcwd()
     os.chdir(dirname)
     yield
@@ -137,14 +148,6 @@ def touch(path):
         os.utime(path, None)
 
 
-def mkdirp(*paths):
-    for path in paths:
-        if not os.path.exists(path):
-            os.makedirs(path)
-        elif not os.path.isdir(path):
-            raise OSError(errno.EEXIST, "File alredy exists", path)
-
-
 def join_path(prefix, *args):
     path = str(prefix)
     for elt in args:
diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 38d5f70282d..f72c7244200 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -153,6 +153,9 @@ def set_module_variables_for_package(pkg):
     m.make  = MakeExecutable('make', pkg.parallel)
     m.gmake = MakeExecutable('gmake', pkg.parallel)
 
+    # easy shortcut to os.environ
+    m.env = os.environ
+
     # number of jobs spack prefers to build with.
     m.make_jobs = multiprocessing.cpu_count()
 
@@ -168,7 +171,7 @@ def set_module_variables_for_package(pkg):
 
     # standard CMake arguments
     m.std_cmake_args = ['-DCMAKE_INSTALL_PREFIX=%s' % pkg.prefix,
-                        '-DCMAKE_BUILD_TYPE=None']
+                        '-DCMAKE_BUILD_TYPE=RelWithDebInfo']
     if platform.mac_ver()[0]:
         m.std_cmake_args.append('-DCMAKE_FIND_FRAMEWORK=LAST')
 
diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py
index 1a1a19a4b62..c98162aca74 100644
--- a/lib/spack/spack/cmd/create.py
+++ b/lib/spack/spack/cmd/create.py
@@ -87,6 +87,9 @@ def setup_parser(subparser):
     subparser.add_argument(
         '--keep-stage', action='store_true', dest='keep_stage',
         help="Don't clean up staging area when command completes.")
+    subparser.add_argument(
+        '-n', '--name', dest='alternate_name', default=None,
+        help="Override the autodetected name for the created package.")
     subparser.add_argument(
         '-f', '--force', action='store_true', dest='force',
         help="Overwrite any existing package file with the same name.")
@@ -121,30 +124,27 @@ def make_version_calls(ver_hash_tuples):
     return '\n'.join(format % ("'%s'" % v, h) for v, h in ver_hash_tuples)
 
 
-def get_name():
-    """Prompt user to input a package name."""
-    name = ""
-    while not name:
-        new_name = raw_input("Name: ")
-        if spack.db.valid_name(name):
-            name = new_name
-        else:
-            print "Package name can only contain A-Z, a-z, 0-9, '_' and '-'"
-    return name
-
-
 def create(parser, args):
     url = args.url
 
     # Try to deduce name and version of the new package from the URL
     name, version = spack.url.parse_name_and_version(url)
-    if not name:
-        tty.msg("Couldn't guess a name for this package.")
-        name = get_name()
+
+    # Use a user-supplied name if one is present
+    name = kwargs.get(args, 'alternate_name', False)
+    if args.name:
+        name = args.name
 
     if not version:
         tty.die("Couldn't guess a version string from %s." % url)
 
+    if not name:
+        tty.die("Couldn't guess a name for this package. Try running:", "",
+                "spack create --name <name> <url>")
+
+    if not spack.db.valid_name(name):
+        tty.die("Package name can only contain A-Z, a-z, 0-9, '_' and '-'")
+
     tty.msg("This looks like a URL for %s version %s." % (name, version))
     tty.msg("Creating template for package %s" % name)
 
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 8df658e6603..0375df7dac5 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -57,7 +57,7 @@
 from spack.util.compression import allowed_archive, extension
 
 """Allowed URL schemes for spack packages."""
-_ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file"]
+_ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"]
 
 
 class Package(object):
diff --git a/lib/spack/spack/util/executable.py b/lib/spack/spack/util/executable.py
index bc27b258895..923c7c19a5b 100644
--- a/lib/spack/spack/util/executable.py
+++ b/lib/spack/spack/util/executable.py
@@ -121,7 +121,7 @@ def which(name, **kwargs):
 
     for dir in path:
         exe = os.path.join(dir, name)
-        if os.access(exe, os.X_OK):
+        if os.path.isfile(exe) and os.access(exe, os.X_OK):
             return Executable(exe)
 
     if required:
diff --git a/var/spack/packages/clang/package.py b/var/spack/packages/clang/package.py
new file mode 100644
index 00000000000..07948a3ed72
--- /dev/null
+++ b/var/spack/packages/clang/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 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 Clang(Package):
+    """The goal of the Clang project is to create a new C, C++,
+       Objective C and Objective C++ front-end for the LLVM compiler.
+    """
+    homepage = "http://clang.llvm.org"
+    url      = "http://llvm.org/releases/3.4.2/cfe-3.4.2.src.tar.gz"
+
+    depends_on("llvm")
+
+    version('3.4.2', '87945973b7c73038871c5f849a818588')
+
+    def install(self, spec, prefix):
+        env['CXXFLAGS'] = '-std=c++11'
+
+        with working_dir('spack-build', create=True):
+            cmake('..',
+                  '-DCLANG_PATH_TO_LLVM_BUILD=%s' % spec['llvm'].prefix,
+                  '-DLLVM_MAIN_SRC_DIR=%s' % spec['llvm'].prefix,
+                  *std_cmake_args)
+            make()
+            make("install")
diff --git a/var/spack/packages/llvm-compiler-rt/package.py b/var/spack/packages/llvm-compiler-rt/package.py
new file mode 100644
index 00000000000..e3fa176afe1
--- /dev/null
+++ b/var/spack/packages/llvm-compiler-rt/package.py
@@ -0,0 +1,57 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 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 LlvmCompilerRt(Package):
+    """Compiler-rt consists of several libraries to be used with LLVM:
+          basics:
+              A simple library that provides an implementation of the
+              low-level target-specific hooks required by code
+              generation and other runtime components.
+
+          sanitizer runtimes:
+              Runtime libraries that are required to run the code with
+              sanitizer instrumentation.
+
+          profiler:
+              Library used to collect coverage information.
+
+          BlocksRuntime:
+              A target-independent implementation of Apple "Blocks"
+              runtime interfaces.
+    """
+    homepage = "http://compiler-rt.llvm.org"
+    url      = "http://llvm.org/releases/3.4/compiler-rt-3.4.src.tar.gz"
+
+    depends_on("clang")
+    depends_on("llvm")
+
+    version('3.4', '7938353e3a3bda85733a165e7ac4bb84')
+
+    def install(self, spec, prefix):
+        cmake(".", *std_cmake_args)
+
+        make()
+        make("install")
diff --git a/var/spack/packages/llvm-lld/package.py b/var/spack/packages/llvm-lld/package.py
new file mode 100644
index 00000000000..ba0b229228e
--- /dev/null
+++ b/var/spack/packages/llvm-lld/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 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 LlvmLld(Package):
+    """lld - The LLVM Linker
+       lld is a new set of modular code for creating linker tools."""
+    homepage = "http://lld.llvm.org"
+    url      = "http://llvm.org/releases/3.4/lld-3.4.src.tar.gz"
+
+    depends_on('llvm')
+
+    version('3.4', '3b6a17e58c8416c869c14dd37682f78e')
+
+    def install(self, spec, prefix):
+        env['CXXFLAGS'] = '-std=c++11'
+
+        with working_dir('spack-build', create=True):
+            cmake('..',
+                  '-DLLD_PATH_TO_LLVM_BUILD=%s' % spec['llvm'].prefix,
+                  '-DLLVM_MAIN_SRC_DIR=%s' % spec['llvm'].prefix,
+                  *std_cmake_args)
+            make('VERBOSE=1')
+            make("install")
diff --git a/var/spack/packages/llvm/package.py b/var/spack/packages/llvm/package.py
index dab10f77d37..08ae7208cd0 100644
--- a/var/spack/packages/llvm/package.py
+++ b/var/spack/packages/llvm/package.py
@@ -37,12 +37,14 @@ class Llvm(Package):
     version('3.4.2', 'a20669f75967440de949ac3b1bad439c')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix,
-            "--enable-optimized",
-            "--enable-debug-runtime",
-            "--enable-debug-symbols",
-            "--disable-assertions",
-            "REQUIRES_RTTI=1")
+        env['CXXFLAGS'] = '-std=c++11'
 
-        make()
-        make("install")
+        with working_dir('spack-build', create=True):
+            cmake('..',
+                  '-DLLVM_REQUIRES_RTTI=1',
+                  '-DPYTHON_EXECUTABLE=/usr/bin/python',
+                  '-DPYTHON_INCLUDE_DIR=/usr/include/python2.6',
+                  '-DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so',
+                  *std_cmake_args)
+            make()
+            make("install")

From d5c625d87d358b7167eb9f985ccd8b1f394a0083 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 7 Aug 2014 19:04:04 -0700
Subject: [PATCH 28/71] Clean up specs, spec comparison, and spec hashing.

- Spec comparison is now less strict
  - compares based on sorted list of dependencies but not
    their structure
  - Makes comparison easy when a spec is not normalized.

- This makes the dep_hash consistent for specs read in from a
  directory layout.  - Can now reliably read in a spec for which the
  package has gone away, and still be able to delete its install.
  - easy switching between git branches

- Fixed latent bug in Spec.flat_dependencies() (was including root)

- added a test for the directory layout so that this code will get
  more exercise.
---
 lib/spack/spack/__init__.py              |   2 +-
 lib/spack/spack/directory_layout.py      |  41 ++++---
 lib/spack/spack/spec.py                  | 105 +++++++++++++----
 lib/spack/spack/test/__init__.py         |   3 +-
 lib/spack/spack/test/directory_layout.py | 141 +++++++++++++++++++++++
 lib/spack/spack/test/spec_dag.py         |  84 ++++++++++----
 6 files changed, 312 insertions(+), 64 deletions(-)
 create mode 100644 lib/spack/spack/test/directory_layout.py

diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py
index 50fe453cfb7..9eae4342e3b 100644
--- a/lib/spack/spack/__init__.py
+++ b/lib/spack/spack/__init__.py
@@ -81,7 +81,7 @@
 # stage directories.
 #
 from spack.directory_layout import SpecHashDirectoryLayout
-install_layout = SpecHashDirectoryLayout(install_path, prefix_size=6)
+install_layout = SpecHashDirectoryLayout(install_path)
 
 #
 # This controls how things are concretized in spack.
diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index 4fc00d536e7..816c945707b 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -30,6 +30,8 @@
 from contextlib import closing
 
 from llnl.util.filesystem import join_path, mkdirp
+
+import spack
 from spack.spec import Spec
 from spack.error import SpackError
 
@@ -131,12 +133,9 @@ def __init__(self, root, **kwargs):
         """Prefix size is number of characters in the SHA-1 prefix to use
            to make each hash unique.
         """
-        prefix_size = kwargs.get('prefix_size', 8)
-        spec_file   = kwargs.get('spec_file', '.spec')
-
+        spec_file_name   = kwargs.get('spec_file_name', '.spec')
         super(SpecHashDirectoryLayout, self).__init__(root)
-        self.prefix_size = prefix_size
-        self.spec_file = spec_file
+        self.spec_file_name = spec_file_name
 
 
     def relative_path_for_spec(self, spec):
@@ -154,16 +153,31 @@ def write_spec(self, spec, path):
     def read_spec(self, path):
         """Read the contents of a file and parse them as a spec"""
         with closing(open(path)) as spec_file:
-            string = spec_file.read().replace('\n', '')
             # Specs from files are assumed normal and concrete
-            return Spec(string, concrete=True)
+            spec = Spec(spec_file.read().replace('\n', ''))
+
+        # If we do not have a package on hand for this spec, we know
+        # it is concrete, and we *assume* that it is normal. This
+        # prevents us from trying to fetch a non-existing package, and
+        # allows best effort for commands like spack find.
+        if not spack.db.exists(spec.name):
+            spec._normal = True
+            spec._concrete = True
+
+        return spec
+
+
+    def spec_file_path(self, spec):
+        """Gets full path to spec file"""
+        _check_concrete(spec)
+        return join_path(self.path_for_spec(spec), self.spec_file_name)
 
 
     def make_path_for_spec(self, spec):
         _check_concrete(spec)
 
         path = self.path_for_spec(spec)
-        spec_file_path = join_path(path, self.spec_file)
+        spec_file_path = self.spec_file_path(spec)
 
         if os.path.isdir(path):
             if not os.path.isfile(spec_file_path):
@@ -177,8 +191,7 @@ def make_path_for_spec(self, spec):
             spec_hash = self.hash_spec(spec)
             installed_hash = self.hash_spec(installed_spec)
             if installed_spec == spec_hash:
-                raise SpecHashCollisionError(
-                    installed_hash, spec_hash, self.prefix_size)
+                raise SpecHashCollisionError(installed_hash, spec_hash)
             else:
                 raise InconsistentInstallDirectoryError(
                     'Spec file in %s does not match SHA-1 hash!'
@@ -195,7 +208,7 @@ def all_specs(self):
         for path in traverse_dirs_at_depth(self.root, 3):
             arch, compiler, last_dir = path
             spec_file_path = join_path(
-                self.root, arch, compiler, last_dir, self.spec_file)
+                self.root, arch, compiler, last_dir, self.spec_file_name)
             if os.path.exists(spec_file_path):
                 spec = self.read_spec(spec_file_path)
                 yield spec
@@ -209,10 +222,10 @@ def __init__(self, message):
 
 class SpecHashCollisionError(DirectoryLayoutError):
     """Raised when there is a hash collision in an SpecHashDirectoryLayout."""
-    def __init__(self, installed_spec, new_spec, prefix_size):
+    def __init__(self, installed_spec, new_spec):
         super(SpecHashDirectoryLayout, self).__init__(
-            'Specs %s and %s have the same %d character SHA-1 prefix!'
-            % prefix_size, installed_spec, new_spec)
+            'Specs %s and %s have the same SHA-1 prefix!'
+            % installed_spec, new_spec)
 
 
 class InconsistentInstallDirectoryError(DirectoryLayoutError):
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index 45c3402617c..fa1962fd138 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -94,6 +94,7 @@
 import itertools
 import hashlib
 from StringIO import StringIO
+from operator import attrgetter
 
 import llnl.util.tty as tty
 from llnl.util.lang import *
@@ -352,10 +353,6 @@ def __init__(self, spec_like, *dep_like, **kwargs):
         self._normal = kwargs.get('normal', False)
         self._concrete = kwargs.get('concrete', False)
 
-        # Specs cannot be concrete and non-normal.
-        if self._concrete:
-            self._normal = True
-
         # This allows users to construct a spec DAG with literals.
         # Note that given two specs a and b, Spec(a) copies a, but
         # Spec(a, b) will copy a but just add b as a dep.
@@ -489,6 +486,8 @@ def preorder_traversal(self, visited=None, d=0, **kwargs):
         """
         depth      = kwargs.get('depth', False)
         key_fun    = kwargs.get('key', id)
+        if isinstance(key_fun, basestring):
+            key_fun = attrgetter(key_fun)
         yield_root = kwargs.get('root', True)
         cover      = kwargs.get('cover', 'nodes')
         direction  = kwargs.get('direction', 'children')
@@ -540,13 +539,15 @@ def prefix(self):
 
 
     def dep_hash(self, length=None):
-        """Return a hash representing the dependencies of this spec
-           This will always normalize first so that the hash is consistent.
+        """Return a hash representing all dependencies of this spec
+           (direct and indirect).
+
+           This always normalizes first so that hash is consistent.
         """
         self.normalize()
 
         sha = hashlib.sha1()
-        sha.update(str(self.dependencies))
+        sha.update(self.dep_string())
         full_hash = sha.hexdigest()
 
         return full_hash[:length]
@@ -661,19 +662,15 @@ def flat_dependencies(self):
 
            This will work even on specs that are not normalized; i.e. specs
            that have two instances of the same dependency in the DAG.
-           This is used as the first step of normalization.
+           This is the first step of normalization.
         """
-        # This ensures that the package descriptions themselves are consistent
-        if not self.virtual:
-            self.package.validate_dependencies()
-
         # Once that is guaranteed, we know any constraint violations are due
         # to the spec -- so they're the user's fault, not Spack's.
         flat_deps = DependencyMap()
         try:
-            for spec in self.preorder_traversal():
+            for spec in self.preorder_traversal(root=False):
                 if spec.name not in flat_deps:
-                    new_spec = spec.copy(dependencies=False)
+                    new_spec = spec.copy(deps=False)
                     flat_deps[spec.name] = new_spec
 
                 else:
@@ -797,9 +794,11 @@ def normalize(self, **kwargs):
         # Ensure first that all packages & compilers in the DAG exist.
         self.validate_names()
 
-        # Then ensure that the packages referenced are sane, that the
-        # provided spec is sane, and that all dependency specs are in the
-        # root node of the spec.  flat_dependencies will do this for us.
+        # Ensure that the package & dep descriptions are consistent & sane
+        if not self.virtual:
+            self.package.validate_dependencies()
+
+        # Get all the dependencies into one DependencyMap
         spec_deps = self.flat_dependencies()
         self.dependencies.clear()
 
@@ -1028,7 +1027,7 @@ def _dup(self, other, **kwargs):
             self.compiler = other.compiler.copy()
 
         self.dependents = DependencyMap()
-        copy_deps = kwargs.get('dependencies', True)
+        copy_deps = kwargs.get('deps', True)
         if copy_deps:
             self.dependencies = other.dependencies.copy()
         else:
@@ -1074,9 +1073,65 @@ def __contains__(self, spec):
         return False
 
 
-    def _cmp_key(self):
+    def sorted_deps(self):
+        """Return a list of all dependencies sorted by name."""
+        deps = self.flat_dependencies()
+        return tuple(deps[name] for name in sorted(deps))
+
+
+    def _eq_dag(self, other, vs, vo):
+        """Test that entire dependency DAGs are equal."""
+        vs.add(id(self))
+        vo.add(id(other))
+
+        if self._cmp_node() != other._cmp_node():
+            return False
+
+        if len(self.dependencies) != len(other.dependencies):
+            return False
+
+        ssorted = [self.dependencies[name]  for name in sorted(self.dependencies)]
+        osorted = [other.dependencies[name] for name in sorted(other.dependencies)]
+
+        for s, o in zip(ssorted, osorted):
+            # Check for duplicate or non-equal dependencies
+            if (id(s) in vs) != (id(o) in vo):
+                return False
+
+            # Skip visited nodes
+            if id(s) in vs:
+                continue
+
+            # Recursive check for equality
+            if not s._eq_dag(o, vs, vo):
+                return False
+
+        return True
+
+
+    def eq_dag(self, other):
+        """True if the entire dependency DAG of this spec is equal to another."""
+        return self._eq_dag(other, set(), set())
+
+
+    def ne_dag(self, other):
+        """True if the entire dependency DAG of this spec is not equal to
+           another."""
+        return not self.eq_dag(other)
+
+
+    def _cmp_node(self):
+        """Comparison key for just *this node* and not its deps."""
         return (self.name, self.versions, self.variants,
-                self.architecture, self.compiler, self.dependencies)
+                self.architecture, self.compiler)
+
+
+    def _cmp_key(self):
+        """Comparison key for this node and all dependencies *without*
+           considering structure.  This is the default, as
+           normalization will restore structure.
+        """
+        return self._cmp_node() + (self.sorted_deps(),)
 
 
     def colorized(self):
@@ -1179,12 +1234,12 @@ def write(s, c):
         return result
 
 
+    def dep_string(self):
+        return ''.join("^" + dep.format() for dep in self.sorted_deps())
+
+
     def __str__(self):
-        by_name = lambda d: d.name
-        deps = self.preorder_traversal(key=by_name, root=False)
-        sorted_deps = sorted(deps, key=by_name)
-        dep_string = ''.join("^" + dep.format() for dep in sorted_deps)
-        return self.format() + dep_string
+        return self.format() + self.dep_string()
 
 
     def tree(self, **kwargs):
diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py
index 5442189c2e5..c2dfc51aa3f 100644
--- a/lib/spack/spack/test/__init__.py
+++ b/lib/spack/spack/test/__init__.py
@@ -45,7 +45,8 @@
               'multimethod',
               'install',
               'package_sanity',
-              'config']
+              'config',
+              'directory_layout']
 
 
 def list_tests():
diff --git a/lib/spack/spack/test/directory_layout.py b/lib/spack/spack/test/directory_layout.py
new file mode 100644
index 00000000000..ca4d4c456c4
--- /dev/null
+++ b/lib/spack/spack/test/directory_layout.py
@@ -0,0 +1,141 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+"""\
+This test verifies that the Spack directory layout works properly.
+"""
+import unittest
+import tempfile
+import shutil
+import os
+
+from llnl.util.filesystem import *
+
+import spack
+from spack.packages import PackageDB
+from spack.directory_layout import SpecHashDirectoryLayout
+
+class DirectoryLayoutTest(unittest.TestCase):
+    """Tests that a directory layout works correctly and produces a
+       consistent install path."""
+
+    def setUp(self):
+        self.tmpdir = tempfile.mkdtemp()
+        self.layout = SpecHashDirectoryLayout(self.tmpdir)
+
+
+    def tearDown(self):
+        shutil.rmtree(self.tmpdir, ignore_errors=True)
+        self.layout = None
+
+
+    def test_read_and_write_spec(self):
+        """This goes through each package in spack and creates a directory for
+           it.  It then ensures that the spec for the directory's
+           installed package can be read back in consistently, and
+           finally that the directory can be removed by the directory
+           layout.
+        """
+        for pkg in spack.db.all_packages():
+            spec = pkg.spec
+
+            # If a spec fails to concretize, just skip it.  If it is a
+            # real error, it will be caught by concretization tests.
+            try:
+                spec.concretize()
+            except:
+                continue
+
+            self.layout.make_path_for_spec(spec)
+
+            install_dir = self.layout.path_for_spec(spec)
+            spec_path = self.layout.spec_file_path(spec)
+
+            # Ensure directory has been created in right place.
+            self.assertTrue(os.path.isdir(install_dir))
+            self.assertTrue(install_dir.startswith(self.tmpdir))
+
+            # Ensure spec file exists when directory is created
+            self.assertTrue(os.path.isfile(spec_path))
+            self.assertTrue(spec_path.startswith(install_dir))
+
+            # Make sure spec file can be read back in to get the original spec
+            spec_from_file = self.layout.read_spec(spec_path)
+            self.assertEqual(spec, spec_from_file)
+
+            # Make sure the dep hash of the read-in spec is the same
+            self.assertEqual(spec.dep_hash(), spec_from_file.dep_hash())
+
+            # Ensure directories are properly removed
+            self.layout.remove_path_for_spec(spec)
+            self.assertFalse(os.path.isdir(install_dir))
+            self.assertFalse(os.path.exists(install_dir))
+
+
+    def test_handle_unknown_package(self):
+        """This test ensures that spack can at least do *some*
+           operations with packages that are installed but that it
+           does not know about.  This is actually not such an uncommon
+           scenario with spack; it can happen when you switch from a
+           git branch where you're working on a new package.
+
+           This test ensures that the directory layout stores enough
+           information about installed packages' specs to uninstall
+           or query them again if the package goes away.
+        """
+        mock_db = PackageDB(spack.mock_packages_path)
+
+        not_in_mock = set(spack.db.all_package_names()).difference(
+            set(mock_db.all_package_names()))
+
+        # Create all the packages that are not in mock.
+        installed_specs = {}
+        for pkg_name in not_in_mock:
+            spec = spack.db.get(pkg_name).spec
+
+            # If a spec fails to concretize, just skip it.  If it is a
+            # real error, it will be caught by concretization tests.
+            try:
+                spec.concretize()
+            except:
+                continue
+
+            self.layout.make_path_for_spec(spec)
+            installed_specs[spec] = self.layout.path_for_spec(spec)
+
+        tmp = spack.db
+        spack.db = mock_db
+
+        # Now check that even without the package files, we know
+        # enough to read a spec from the spec file.
+        for spec, path in installed_specs.items():
+            spec_from_file = self.layout.read_spec(join_path(path, '.spec'))
+
+            # To satisfy these conditions, directory layouts need to
+            # read in concrete specs from their install dirs somehow.
+            self.assertEqual(path, self.layout.path_for_spec(spec_from_file))
+            self.assertEqual(spec, spec_from_file)
+            self.assertEqual(spec.dep_hash(), spec_from_file.dep_hash())
+
+        spack.db = tmp
diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py
index 0c0b214ab71..e9cdfee8b1b 100644
--- a/lib/spack/spack/test/spec_dag.py
+++ b/lib/spack/spack/test/spec_dag.py
@@ -221,30 +221,53 @@ def test_invalid_dep(self):
 
 
     def test_equal(self):
-        spec = Spec('mpileaks ^callpath ^libelf ^libdwarf')
-        self.assertNotEqual(spec, Spec(
-            'mpileaks', Spec('callpath',
-                             Spec('libdwarf',
-                                  Spec('libelf')))))
-        self.assertNotEqual(spec, Spec(
-            'mpileaks', Spec('callpath',
-                             Spec('libelf',
-                                  Spec('libdwarf')))))
+        # Different spec structures to test for equality
+        flat = Spec('mpileaks ^callpath ^libelf ^libdwarf')
 
-        self.assertEqual(spec, Spec(
-            'mpileaks', Spec('callpath'), Spec('libdwarf'), Spec('libelf')))
+        flat_init = Spec(
+            'mpileaks', Spec('callpath'), Spec('libdwarf'), Spec('libelf'))
 
-        self.assertEqual(spec, Spec(
-            'mpileaks', Spec('libelf'), Spec('libdwarf'), Spec('callpath')))
+        flip_flat = Spec(
+            'mpileaks', Spec('libelf'), Spec('libdwarf'), Spec('callpath'))
+
+        dag = Spec('mpileaks', Spec('callpath',
+                                    Spec('libdwarf',
+                                         Spec('libelf'))))
+
+        flip_dag = Spec('mpileaks', Spec('callpath',
+                                         Spec('libelf',
+                                              Spec('libdwarf'))))
+
+        # All these are equal to each other with regular ==
+        specs = (flat, flat_init, flip_flat, dag, flip_dag)
+        for lhs, rhs in zip(specs, specs):
+            self.assertEqual(lhs, rhs)
+            self.assertEqual(str(lhs), str(rhs))
+
+        # Same DAGs constructed different ways are equal
+        self.assertTrue(flat.eq_dag(flat_init))
+
+        # order at same level does not matter -- (dep on same parent)
+        self.assertTrue(flat.eq_dag(flip_flat))
+
+        # DAGs should be unequal if nesting is different
+        self.assertFalse(flat.eq_dag(dag))
+        self.assertFalse(flat.eq_dag(flip_dag))
+        self.assertFalse(flip_flat.eq_dag(dag))
+        self.assertFalse(flip_flat.eq_dag(flip_dag))
+        self.assertFalse(dag.eq_dag(flip_dag))
 
 
     def test_normalize_mpileaks(self):
+        # Spec parsed in from a string
         spec = Spec('mpileaks ^mpich ^callpath ^dyninst ^libelf@1.8.11 ^libdwarf')
 
+        # What that spec should look like after parsing
         expected_flat = Spec(
             'mpileaks', Spec('mpich'), Spec('callpath'), Spec('dyninst'),
             Spec('libelf@1.8.11'), Spec('libdwarf'))
 
+        # What it should look like after normalization
         mpich = Spec('mpich')
         libelf = Spec('libelf@1.8.11')
         expected_normalized = Spec(
@@ -257,7 +280,10 @@ def test_normalize_mpileaks(self):
                  mpich),
             mpich)
 
-        expected_non_unique_nodes = Spec(
+        # Similar to normalized spec, but now with copies of the same
+        # libelf node.  Normalization should result in a single unique
+        # node for each package, so this is the wrong DAG.
+        non_unique_nodes = Spec(
             'mpileaks',
             Spec('callpath',
                  Spec('dyninst',
@@ -267,21 +293,33 @@ def test_normalize_mpileaks(self):
                  mpich),
             Spec('mpich'))
 
-        self.assertEqual(expected_normalized, expected_non_unique_nodes)
-
-        self.assertEqual(str(expected_normalized), str(expected_non_unique_nodes))
-        self.assertEqual(str(spec), str(expected_non_unique_nodes))
-        self.assertEqual(str(expected_normalized), str(spec))
+        # All specs here should be equal under regular equality
+        specs = (spec, expected_flat, expected_normalized, non_unique_nodes)
+        for lhs, rhs in zip(specs, specs):
+            self.assertEqual(lhs, rhs)
+            self.assertEqual(str(lhs), str(rhs))
 
+        # Test that equal and equal_dag are doing the right thing
         self.assertEqual(spec, expected_flat)
-        self.assertNotEqual(spec, expected_normalized)
-        self.assertNotEqual(spec, expected_non_unique_nodes)
+        self.assertTrue(spec.eq_dag(expected_flat))
+
+        self.assertEqual(spec, expected_normalized)
+        self.assertFalse(spec.eq_dag(expected_normalized))
+
+        self.assertEqual(spec, non_unique_nodes)
+        self.assertFalse(spec.eq_dag(non_unique_nodes))
 
         spec.normalize()
 
-        self.assertNotEqual(spec, expected_flat)
+        # After normalizing, spec_dag_equal should match the normalized spec.
+        self.assertEqual(spec, expected_flat)
+        self.assertFalse(spec.eq_dag(expected_flat))
+
         self.assertEqual(spec, expected_normalized)
-        self.assertEqual(spec, expected_non_unique_nodes)
+        self.assertTrue(spec.eq_dag(expected_normalized))
+
+        self.assertEqual(spec, non_unique_nodes)
+        self.assertFalse(spec.eq_dag(non_unique_nodes))
 
 
     def test_normalize_with_virtual_package(self):

From 63f8af8078120be64f69a855e3547a334f96acaf Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Fri, 8 Aug 2014 13:18:20 -0700
Subject: [PATCH 29/71] Add postorder traversal to specs

- Spec.preorder_traversal() is now Spec.traverse().
- Caller can supply order='pre' or order='post'
---
 lib/spack/spack/concretize.py    |   2 +-
 lib/spack/spack/spec.py          | 131 +++++++++++++++++++------------
 lib/spack/spack/test/spec_dag.py |  67 +++++++++++++---
 3 files changed, 138 insertions(+), 62 deletions(-)

diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py
index eb497711b72..e6d1bb87d4e 100644
--- a/lib/spack/spack/concretize.py
+++ b/lib/spack/spack/concretize.py
@@ -118,7 +118,7 @@ def concretize_compiler(self, spec):
             return
 
         try:
-            nearest = next(p for p in spec.preorder_traversal(direction='parents')
+            nearest = next(p for p in spec.traverse(direction='parents')
                            if p.compiler is not None).compiler
 
             if not nearest in all_compilers:
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index fa1962fd138..9c88c800242 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -451,10 +451,19 @@ def concrete(self):
         return self._concrete
 
 
-    def preorder_traversal(self, visited=None, d=0, **kwargs):
-        """Generic preorder traversal of the DAG represented by this spec.
+    def traverse(self, visited=None, d=0, **kwargs):
+        """Generic traversal of the DAG represented by this spec.
            This will yield each node in the spec.  Options:
 
+           order    [=pre|post]
+               Order to traverse spec nodes. Defaults to preorder traversal.
+               Options are:
+
+               'pre':  Pre-order traversal; each node is yielded before its
+                       children in the dependency DAG.
+               'post': Post-order  traversal; each node is yielded after its
+                       children in the dependency DAG.
+
            cover    [=nodes|edges|paths]
                Determines how extensively to cover the dag.  Possible vlaues:
 
@@ -472,7 +481,7 @@ def preorder_traversal(self, visited=None, d=0, **kwargs):
                spec, but also their depth from the root in a (depth, node)
                tuple.
 
-           keyfun   [=id]
+           key   [=id]
                Allow a custom key function to track the identity of nodes
                in the traversal.
 
@@ -484,6 +493,7 @@ def preorder_traversal(self, visited=None, d=0, **kwargs):
                'parents', traverses upwards in the DAG towards the root.
 
         """
+        # get initial values for kwargs
         depth      = kwargs.get('depth', False)
         key_fun    = kwargs.get('key', id)
         if isinstance(key_fun, basestring):
@@ -491,39 +501,49 @@ def preorder_traversal(self, visited=None, d=0, **kwargs):
         yield_root = kwargs.get('root', True)
         cover      = kwargs.get('cover', 'nodes')
         direction  = kwargs.get('direction', 'children')
+        order      = kwargs.get('order', 'pre')
 
-        cover_values = ('nodes', 'edges', 'paths')
-        if cover not in cover_values:
-            raise ValueError("Invalid value for cover: %s.  Choices are %s"
-                             % (cover, ",".join(cover_values)))
-
-        direction_values = ('children', 'parents')
-        if direction not in direction_values:
-            raise ValueError("Invalid value for direction: %s.  Choices are %s"
-                             % (direction, ",".join(direction_values)))
+        # Make sure kwargs have legal values; raise ValueError if not.
+        def validate(name, val, allowed_values):
+            if val not in allowed_values:
+                raise ValueError("Invalid value for %s: %s.  Choices are %s"
+                                 % (name, val, ",".join(allowed_values)))
+        validate('cover',     cover,     ('nodes', 'edges', 'paths'))
+        validate('direction', direction, ('children', 'parents'))
+        validate('order',     order,     ('pre', 'post'))
 
         if visited is None:
             visited = set()
-
-        result = (d, self) if depth else self
         key = key_fun(self)
 
-        if key in visited:
-            if cover == 'nodes':    return
-            if yield_root or d > 0: yield result
-            if cover == 'edges':    return
-        else:
-            if yield_root or d > 0: yield result
+        # Node traversal does not yield visited nodes.
+        if key in visited and cover == 'nodes':
+            return
 
-        successors = self.dependencies
-        if direction == 'parents':
-            successors = self.dependents
+        # Determine whether and what to yield for this node.
+        yield_me = yield_root or d > 0
+        result = (d, self) if depth else self
 
-        visited.add(key)
-        for name in sorted(successors):
-            child = successors[name]
-            for elt in child.preorder_traversal(visited, d+1, **kwargs):
-                yield elt
+        # Preorder traversal yields before successors
+        if yield_me and order == 'pre':
+            yield result
+
+        # Edge traversal yields but skips children of visited nodes
+        if not (key in visited and cover == 'edges'):
+            # This code determines direction and yields the children/parents
+            successors = self.dependencies
+            if direction == 'parents':
+                successors = self.dependents
+
+            visited.add(key)
+            for name in sorted(successors):
+                child = successors[name]
+                for elt in child.traverse(visited, d+1, **kwargs):
+                    yield elt
+
+        # Postorder traversal yields after successors
+        if yield_me and order == 'post':
+            yield result
 
 
     @property
@@ -610,7 +630,7 @@ def _expand_virtual_packages(self):
               a problem.
         """
         while True:
-            virtuals =[v for v in self.preorder_traversal() if v.virtual]
+            virtuals =[v for v in self.traverse() if v.virtual]
             if not virtuals:
                 return
 
@@ -668,7 +688,7 @@ def flat_dependencies(self):
         # to the spec -- so they're the user's fault, not Spack's.
         flat_deps = DependencyMap()
         try:
-            for spec in self.preorder_traversal(root=False):
+            for spec in self.traverse(root=False):
                 if spec.name not in flat_deps:
                     new_spec = spec.copy(deps=False)
                     flat_deps[spec.name] = new_spec
@@ -842,7 +862,7 @@ def validate_names(self):
            If they're not, it will raise either UnknownPackageError or
            UnsupportedCompilerError.
         """
-        for spec in self.preorder_traversal():
+        for spec in self.traverse():
             # Don't get a package for a virtual name.
             if not spec.virtual:
                 spack.db.get(spec.name)
@@ -910,17 +930,17 @@ def _constrain_dependencies(self, other):
     def common_dependencies(self, other):
         """Return names of dependencies that self an other have in common."""
         common = set(
-            s.name for s in self.preorder_traversal(root=False))
+            s.name for s in self.traverse(root=False))
         common.intersection_update(
-            s.name for s in other.preorder_traversal(root=False))
+            s.name for s in other.traverse(root=False))
         return common
 
 
     def dep_difference(self, other):
         """Returns dependencies in self that are not in other."""
-        mine = set(s.name for s in self.preorder_traversal(root=False))
+        mine = set(s.name for s in self.traverse(root=False))
         mine.difference_update(
-            s.name for s in other.preorder_traversal(root=False))
+            s.name for s in other.traverse(root=False))
         return mine
 
 
@@ -979,8 +999,8 @@ def satisfies_dependencies(self, other):
                 return False
 
         # For virtual dependencies, we need to dig a little deeper.
-        self_index = ProviderIndex(self.preorder_traversal(), restrict=True)
-        other_index = ProviderIndex(other.preorder_traversal(), restrict=True)
+        self_index = ProviderIndex(self.traverse(), restrict=True)
+        other_index = ProviderIndex(other.traverse(), restrict=True)
 
         # This handles cases where there are already providers for both vpkgs
         if not self_index.satisfies(other_index):
@@ -1002,7 +1022,7 @@ def satisfies_dependencies(self, other):
 
     def virtual_dependencies(self):
         """Return list of any virtual deps in this spec."""
-        return [spec for spec in self.preorder_traversal() if spec.virtual]
+        return [spec for spec in self.traverse() if spec.virtual]
 
 
     def _dup(self, other, **kwargs):
@@ -1056,7 +1076,7 @@ def version(self):
 
     def __getitem__(self, name):
         """TODO: reconcile __getitem__, _add_dependency, __contains__"""
-        for spec in self.preorder_traversal():
+        for spec in self.traverse():
             if spec.name == name:
                 return spec
 
@@ -1067,7 +1087,7 @@ def __contains__(self, spec):
         """True if this spec has any dependency that satisfies the supplied
            spec."""
         spec = self._autospec(spec)
-        for s in self.preorder_traversal():
+        for s in self.traverse():
             if s.satisfies(spec):
                 return True
         return False
@@ -1080,11 +1100,12 @@ def sorted_deps(self):
 
 
     def _eq_dag(self, other, vs, vo):
-        """Test that entire dependency DAGs are equal."""
+        """Recursive helper for eq_dag and ne_dag.  Does the actual DAG
+           traversal."""
         vs.add(id(self))
         vo.add(id(other))
 
-        if self._cmp_node() != other._cmp_node():
+        if self.ne_node(other):
             return False
 
         if len(self.dependencies) != len(other.dependencies):
@@ -1094,13 +1115,14 @@ def _eq_dag(self, other, vs, vo):
         osorted = [other.dependencies[name] for name in sorted(other.dependencies)]
 
         for s, o in zip(ssorted, osorted):
+            visited_s = id(s) in vs
+            visited_o = id(o) in vo
+
             # Check for duplicate or non-equal dependencies
-            if (id(s) in vs) != (id(o) in vo):
-                return False
+            if visited_s != visited_o: return False
 
             # Skip visited nodes
-            if id(s) in vs:
-                continue
+            if visited_s or visited_o: continue
 
             # Recursive check for equality
             if not s._eq_dag(o, vs, vo):
@@ -1110,13 +1132,12 @@ def _eq_dag(self, other, vs, vo):
 
 
     def eq_dag(self, other):
-        """True if the entire dependency DAG of this spec is equal to another."""
+        """True if the full dependency DAGs of specs are equal"""
         return self._eq_dag(other, set(), set())
 
 
     def ne_dag(self, other):
-        """True if the entire dependency DAG of this spec is not equal to
-           another."""
+        """True if the full dependency DAGs of specs are not equal"""
         return not self.eq_dag(other)
 
 
@@ -1126,6 +1147,16 @@ def _cmp_node(self):
                 self.architecture, self.compiler)
 
 
+    def eq_node(self, other):
+        """Equality with another spec, not including dependencies."""
+        return self._cmp_node() == other._cmp_node()
+
+
+    def ne_node(self, other):
+        """Inequality with another spec, not including dependencies."""
+        return self._cmp_node() != other._cmp_node()
+
+
     def _cmp_key(self):
         """Comparison key for this node and all dependencies *without*
            considering structure.  This is the default, as
@@ -1255,7 +1286,7 @@ def tree(self, **kwargs):
         out = ""
         cur_id = 0
         ids = {}
-        for d, node in self.preorder_traversal(cover=cover, depth=True):
+        for d, node in self.traverse(order='pre', cover=cover, depth=True):
             out += " " * indent
             if depth:
                 out += "%-4d" % d
diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py
index e9cdfee8b1b..966d4b0919e 100644
--- a/lib/spack/spack/test/spec_dag.py
+++ b/lib/spack/spack/test/spec_dag.py
@@ -48,7 +48,7 @@ def test_conflicting_package_constraints(self):
                           spec.package.validate_dependencies)
 
 
-    def test_unique_node_traversal(self):
+    def test_preorder_node_traversal(self):
         dag = Spec('mpileaks ^zmpi')
         dag.normalize()
 
@@ -56,14 +56,14 @@ def test_unique_node_traversal(self):
                  'zmpi', 'fake']
         pairs = zip([0,1,2,3,4,2,3], names)
 
-        traversal = dag.preorder_traversal()
+        traversal = dag.traverse()
         self.assertListEqual([x.name for x in traversal], names)
 
-        traversal = dag.preorder_traversal(depth=True)
+        traversal = dag.traverse(depth=True)
         self.assertListEqual([(x, y.name) for x,y in traversal], pairs)
 
 
-    def test_unique_edge_traversal(self):
+    def test_preorder_edge_traversal(self):
         dag = Spec('mpileaks ^zmpi')
         dag.normalize()
 
@@ -71,14 +71,14 @@ def test_unique_edge_traversal(self):
                  'libelf', 'zmpi', 'fake', 'zmpi']
         pairs = zip([0,1,2,3,4,3,2,3,1], names)
 
-        traversal = dag.preorder_traversal(cover='edges')
+        traversal = dag.traverse(cover='edges')
         self.assertListEqual([x.name for x in traversal], names)
 
-        traversal = dag.preorder_traversal(cover='edges', depth=True)
+        traversal = dag.traverse(cover='edges', depth=True)
         self.assertListEqual([(x, y.name) for x,y in traversal], pairs)
 
 
-    def test_unique_path_traversal(self):
+    def test_preorder_path_traversal(self):
         dag = Spec('mpileaks ^zmpi')
         dag.normalize()
 
@@ -86,10 +86,55 @@ def test_unique_path_traversal(self):
                  'libelf', 'zmpi', 'fake', 'zmpi', 'fake']
         pairs = zip([0,1,2,3,4,3,2,3,1,2], names)
 
-        traversal = dag.preorder_traversal(cover='paths')
+        traversal = dag.traverse(cover='paths')
         self.assertListEqual([x.name for x in traversal], names)
 
-        traversal = dag.preorder_traversal(cover='paths', depth=True)
+        traversal = dag.traverse(cover='paths', depth=True)
+        self.assertListEqual([(x, y.name) for x,y in traversal], pairs)
+
+
+    def test_postorder_node_traversal(self):
+        dag = Spec('mpileaks ^zmpi')
+        dag.normalize()
+
+        names = ['libelf', 'libdwarf', 'dyninst', 'fake', 'zmpi',
+                 'callpath', 'mpileaks']
+        pairs = zip([4,3,2,3,2,1,0], names)
+
+        traversal = dag.traverse(order='post')
+        self.assertListEqual([x.name for x in traversal], names)
+
+        traversal = dag.traverse(depth=True, order='post')
+        self.assertListEqual([(x, y.name) for x,y in traversal], pairs)
+
+
+    def test_postorder_edge_traversal(self):
+        dag = Spec('mpileaks ^zmpi')
+        dag.normalize()
+
+        names = ['libelf', 'libdwarf', 'libelf', 'dyninst', 'fake', 'zmpi',
+                 'callpath', 'zmpi', 'mpileaks']
+        pairs = zip([4,3,3,2,3,2,1,1,0], names)
+
+        traversal = dag.traverse(cover='edges', order='post')
+        self.assertListEqual([x.name for x in traversal], names)
+
+        traversal = dag.traverse(cover='edges', depth=True, order='post')
+        self.assertListEqual([(x, y.name) for x,y in traversal], pairs)
+
+
+    def test_postorder_path_traversal(self):
+        dag = Spec('mpileaks ^zmpi')
+        dag.normalize()
+
+        names = ['libelf', 'libdwarf', 'libelf', 'dyninst', 'fake', 'zmpi',
+                 'callpath', 'fake', 'zmpi', 'mpileaks']
+        pairs = zip([4,3,3,2,3,2,1,2,1,0], names)
+
+        traversal = dag.traverse(cover='paths', order='post')
+        self.assertListEqual([x.name for x in traversal], names)
+
+        traversal = dag.traverse(cover='paths', depth=True, order='post')
         self.assertListEqual([(x, y.name) for x,y in traversal], pairs)
 
 
@@ -142,7 +187,7 @@ def test_normalize_with_virtual_spec(self):
 
         # make sure nothing with the same name occurs twice
         counts = {}
-        for spec in dag.preorder_traversal(keyfun=id):
+        for spec in dag.traverse(key=id):
             if not spec.name in counts:
                 counts[spec.name] = 0
             counts[spec.name] += 1
@@ -152,7 +197,7 @@ def test_normalize_with_virtual_spec(self):
 
 
     def check_links(self, spec_to_check):
-        for spec in spec_to_check.preorder_traversal():
+        for spec in spec_to_check.traverse():
             for dependent in spec.dependents.values():
                 self.assertIn(
                     spec.name, dependent.dependencies,

From 5f073ae220058331b10423d65b3bcc20406a4d9f Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 9 Aug 2014 16:17:40 -0700
Subject: [PATCH 30/71] More spec improvements

- Spec.copy() does not create superfluous nodes and preserves DAG
  connections.

- Spec.normalize() doesn't create extra dependency nodes or throw out
  old ones like before.

- Added better test cases for above changes.

Minor things:
- Fixed bug waiting to happen in PackageDB.get()
  - instances was keyed by name, not by spec, so caching wasn't really
    working at all.
- removed unused PackageDB.compute_dependents function.
- Fixed PackageDB.graph_dependencies() so that spack graph works again.
---
 lib/spack/spack/cmd/dependents.py        |  6 +-
 lib/spack/spack/packages.py              | 31 +++-----
 lib/spack/spack/spec.py                  | 90 ++++++++++++++----------
 lib/spack/spack/test/directory_layout.py | 14 ++++
 lib/spack/spack/test/spec_dag.py         | 53 ++++++++++++++
 5 files changed, 131 insertions(+), 63 deletions(-)

diff --git a/lib/spack/spack/cmd/dependents.py b/lib/spack/spack/cmd/dependents.py
index db6be88d321..129a4eeb237 100644
--- a/lib/spack/spack/cmd/dependents.py
+++ b/lib/spack/spack/cmd/dependents.py
@@ -29,7 +29,7 @@
 import spack
 import spack.cmd
 
-description = "Show dependent packages."
+description = "Show installed packages that depend on another."
 
 def setup_parser(subparser):
     subparser.add_argument(
@@ -42,5 +42,5 @@ def dependents(parser, args):
         tty.die("spack dependents takes only one spec.")
 
     fmt = '$_$@$%@$+$=$#'
-    deps = [d.format(fmt) for d in specs[0].package.installed_dependents]
-    tty.msg("Dependents of %s" % specs[0].format(fmt), *deps)
+    deps = [d.format(fmt, color=True) for d in specs[0].package.installed_dependents]
+    tty.msg("Dependents of %s" % specs[0].format(fmt, color=True), *deps)
diff --git a/lib/spack/spack/packages.py b/lib/spack/spack/packages.py
index 00834c95d54..744ccae2d1b 100644
--- a/lib/spack/spack/packages.py
+++ b/lib/spack/spack/packages.py
@@ -69,9 +69,9 @@ def get(self, spec):
 
         if not spec in self.instances:
             package_class = self.get_class_for_package_name(spec.name)
-            self.instances[spec.name] = package_class(spec)
+            self.instances[spec.copy()] = package_class(spec)
 
-        return self.instances[spec.name]
+        return self.instances[spec]
 
 
     @_autospec
@@ -179,24 +179,6 @@ def get_class_for_package_name(self, pkg_name):
         return cls
 
 
-    def compute_dependents(self):
-        """Reads in all package files and sets dependence information on
-           Package objects in memory.
-        """
-        if not hasattr(compute_dependents, index):
-            compute_dependents.index = {}
-
-        for pkg in all_packages():
-            if pkg._dependents is None:
-                pkg._dependents = []
-
-            for name, dep in pkg.dependencies.iteritems():
-                dpkg = self.get(name)
-                if dpkg._dependents is None:
-                    dpkg._dependents = []
-                dpkg._dependents.append(pkg.name)
-
-
     def graph_dependencies(self, out=sys.stdout):
         """Print out a graph of all the dependencies between package.
            Graph is in dot format."""
@@ -211,10 +193,17 @@ def quote(string):
             return '"%s"' % string
 
         deps = []
-        for pkg in all_packages():
+        for pkg in self.all_packages():
             out.write('  %-30s [label="%s"]\n' % (quote(pkg.name), pkg.name))
+
+            # Add edges for each depends_on in the package.
             for dep_name, dep in pkg.dependencies.iteritems():
                 deps.append((pkg.name, dep_name))
+
+            # If the package provides something, add an edge for that.
+            for provider in set(p.name for p in pkg.provided):
+                deps.append((provider, pkg.name))
+
         out.write('\n')
 
         for pair in deps:
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index 9c88c800242..aa6397271b7 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -310,9 +310,8 @@ def concrete(self):
 
 
     def __str__(self):
-        sorted_dep_names = sorted(self.keys())
         return ''.join(
-            ["^" + str(self[name]) for name in sorted_dep_names])
+            ["^" + str(self[name]) for name in sorted(self.keys())])
 
 
 @key_ordering
@@ -562,10 +561,9 @@ def dep_hash(self, length=None):
         """Return a hash representing all dependencies of this spec
            (direct and indirect).
 
-           This always normalizes first so that hash is consistent.
+           If you want this hash to be consistent, you should
+           concretize the spec first so that it is not ambiguous.
         """
-        self.normalize()
-
         sha = hashlib.sha1()
         sha.update(self.dep_string())
         full_hash = sha.hexdigest()
@@ -641,7 +639,7 @@ def _expand_virtual_packages(self):
                 spec._replace_with(concrete)
 
             # If there are duplicate providers or duplicate provider deps, this
-            # consolidates them and merges constraints.
+            # consolidates them and merge constraints.
             self.normalize(force=True)
 
 
@@ -675,43 +673,51 @@ def concretized(self):
         return clone
 
 
-    def flat_dependencies(self):
-        """Return a DependencyMap containing all of this spec's dependencies
-           with their constraints merged.  If there are any conflicts, throw
-           an exception.
+    def flat_dependencies(self, **kwargs):
+        """Return a DependencyMap containing all of this spec's
+           dependencies with their constraints merged.
 
-           This will work even on specs that are not normalized; i.e. specs
-           that have two instances of the same dependency in the DAG.
-           This is the first step of normalization.
+           If copy is True, returns merged copies of its dependencies
+           without modifying the spec it's called on.
+
+           If copy is False, clears this spec's dependencies and
+           returns them.
         """
-        # Once that is guaranteed, we know any constraint violations are due
-        # to the spec -- so they're the user's fault, not Spack's.
+        copy = kwargs.get('copy', True)
+
         flat_deps = DependencyMap()
         try:
             for spec in self.traverse(root=False):
                 if spec.name not in flat_deps:
-                    new_spec = spec.copy(deps=False)
-                    flat_deps[spec.name] = new_spec
-
+                    if copy:
+                        flat_deps[spec.name] = spec.copy(deps=False)
+                    else:
+                        flat_deps[spec.name] = spec
                 else:
                     flat_deps[spec.name].constrain(spec)
 
-        except UnsatisfiableSpecError, e:
-            # This REALLY shouldn't happen unless something is wrong in spack.
-            # It means we got a spec DAG with two instances of the same package
-            # that had inconsistent constraints.  There's no way for a user to
-            # produce a spec like this (the parser adds all deps to the root),
-            # so this means OUR code is not sane!
-            raise InconsistentSpecError("Invalid Spec DAG: %s" % e.message)
+            if not copy:
+                for dep in flat_deps.values():
+                    dep.dependencies.clear()
+                    dep.dependents.clear()
+                self.dependencies.clear()
 
-        return flat_deps
+            return flat_deps
+
+        except UnsatisfiableSpecError, e:
+            # Here, the DAG contains two instances of the same package
+            # with inconsistent constraints.  Users cannot produce
+            # inconsistent specs like this on the command line: the
+            # parser doesn't allow it. Spack must be broken!
+            raise InconsistentSpecError("Invalid Spec DAG: %s" % e.message)
 
 
     def flatten(self):
         """Pull all dependencies up to the root (this spec).
            Merge constraints for dependencies with the same name, and if they
            conflict, throw an exception. """
-        self.dependencies = self.flat_dependencies()
+        for dep in self.flat_dependencies(copy=False):
+            self._add_dependency(dep)
 
 
     def _normalize_helper(self, visited, spec_deps, provider_index):
@@ -819,8 +825,7 @@ def normalize(self, **kwargs):
             self.package.validate_dependencies()
 
         # Get all the dependencies into one DependencyMap
-        spec_deps = self.flat_dependencies()
-        self.dependencies.clear()
+        spec_deps = self.flat_dependencies(copy=False)
 
         # Figure out which of the user-provided deps provide virtual deps.
         # Remove virtual deps that are already provided by something in the spec
@@ -1037,22 +1042,29 @@ def _dup(self, other, **kwargs):
                Whether deps should be copied too.  Set to false to copy a
                spec but not its dependencies.
         """
-        # TODO: this needs to handle DAGs.
+        # Local node attributes get copied first.
         self.name = other.name
         self.versions = other.versions.copy()
         self.variants = other.variants.copy()
         self.architecture = other.architecture
-        self.compiler = None
-        if other.compiler:
-            self.compiler = other.compiler.copy()
-
+        self.compiler = other.compiler.copy() if other.compiler else None
         self.dependents = DependencyMap()
-        copy_deps = kwargs.get('deps', True)
-        if copy_deps:
-            self.dependencies = other.dependencies.copy()
-        else:
-            self.dependencies = DependencyMap()
+        self.dependencies = DependencyMap()
 
+        # If we copy dependencies, preserve DAG structure in the new spec
+        if kwargs.get('deps', True):
+            # This copies the deps from other using _dup(deps=False)
+            new_nodes = other.flat_dependencies()
+            new_nodes[self.name] = self
+
+            # Hook everything up properly here by traversing.
+            for spec in other.traverse(cover='nodes'):
+                parent = new_nodes[spec.name]
+                for child in spec.dependencies:
+                    if child not in parent.dependencies:
+                        parent._add_dependency(new_nodes[child])
+
+        # Since we preserved structure, we can copy _normal safely.
         self._normal = other._normal
         self._concrete = other._concrete
 
diff --git a/lib/spack/spack/test/directory_layout.py b/lib/spack/spack/test/directory_layout.py
index ca4d4c456c4..3e52954cfe2 100644
--- a/lib/spack/spack/test/directory_layout.py
+++ b/lib/spack/spack/test/directory_layout.py
@@ -29,10 +29,12 @@
 import tempfile
 import shutil
 import os
+from contextlib import closing
 
 from llnl.util.filesystem import *
 
 import spack
+from spack.spec import Spec
 from spack.packages import PackageDB
 from spack.directory_layout import SpecHashDirectoryLayout
 
@@ -83,6 +85,18 @@ def test_read_and_write_spec(self):
             # Make sure spec file can be read back in to get the original spec
             spec_from_file = self.layout.read_spec(spec_path)
             self.assertEqual(spec, spec_from_file)
+            self.assertTrue(spec.eq_dag, spec_from_file)
+            self.assertTrue(spec_from_file.concrete)
+
+            # Ensure that specs that come out "normal" are really normal.
+            with closing(open(spec_path)) as spec_file:
+                read_separately = Spec(spec_file.read())
+
+                read_separately.normalize()
+                self.assertEqual(read_separately, spec_from_file)
+
+                read_separately.concretize()
+                self.assertEqual(read_separately, spec_from_file)
 
             # Make sure the dep hash of the read-in spec is the same
             self.assertEqual(spec.dep_hash(), spec_from_file.dep_hash())
diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py
index 966d4b0919e..322f34cf024 100644
--- a/lib/spack/spack/test/spec_dag.py
+++ b/lib/spack/spack/test/spec_dag.py
@@ -392,3 +392,56 @@ def test_contains(self):
         self.assertIn(Spec('libdwarf'), spec)
         self.assertNotIn(Spec('libgoblin'), spec)
         self.assertIn(Spec('mpileaks'), spec)
+
+
+    def test_copy_simple(self):
+        orig = Spec('mpileaks')
+        copy = orig.copy()
+
+        self.check_links(copy)
+
+        self.assertEqual(orig, copy)
+        self.assertTrue(orig.eq_dag(copy))
+        self.assertEqual(orig._normal, copy._normal)
+        self.assertEqual(orig._concrete, copy._concrete)
+
+        # ensure no shared nodes bt/w orig and copy.
+        orig_ids = set(id(s) for s in orig.traverse())
+        copy_ids = set(id(s) for s in copy.traverse())
+        self.assertFalse(orig_ids.intersection(copy_ids))
+
+
+    def test_copy_normalized(self):
+        orig = Spec('mpileaks')
+        orig.normalize()
+        copy = orig.copy()
+
+        self.check_links(copy)
+
+        self.assertEqual(orig, copy)
+        self.assertTrue(orig.eq_dag(copy))
+        self.assertEqual(orig._normal, copy._normal)
+        self.assertEqual(orig._concrete, copy._concrete)
+
+        # ensure no shared nodes bt/w orig and copy.
+        orig_ids = set(id(s) for s in orig.traverse())
+        copy_ids = set(id(s) for s in copy.traverse())
+        self.assertFalse(orig_ids.intersection(copy_ids))
+
+
+    def test_copy_concretized(self):
+        orig = Spec('mpileaks')
+        orig.concretize()
+        copy = orig.copy()
+
+        self.check_links(copy)
+
+        self.assertEqual(orig, copy)
+        self.assertTrue(orig.eq_dag(copy))
+        self.assertEqual(orig._normal, copy._normal)
+        self.assertEqual(orig._concrete, copy._concrete)
+
+        # ensure no shared nodes bt/w orig and copy.
+        orig_ids = set(id(s) for s in orig.traverse())
+        copy_ids = set(id(s) for s in copy.traverse())
+        self.assertFalse(orig_ids.intersection(copy_ids))

From 98797459f343c400f4f6fe988bae47d4bab9116b Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 9 Aug 2014 17:41:56 -0700
Subject: [PATCH 31/71] Minor tweaks after spec update.

- spack find -p works properly (get path from spec, not package)

- directory layout and PackageDB normalize things automatically unless
  they're unknown packages (need to do this for spack find -l)

- install test made robust to mock/main package conflicts
---
 lib/spack/spack/cmd/find.py         |  2 +-
 lib/spack/spack/directory_layout.py |  6 ++++++
 lib/spack/spack/packages.py         |  8 +++++++-
 lib/spack/spack/test/install.py     | 16 +++++++++++++++-
 4 files changed, 29 insertions(+), 3 deletions(-)

diff --git a/lib/spack/spack/cmd/find.py b/lib/spack/spack/cmd/find.py
index 7f2bce119e2..72df69d18a8 100644
--- a/lib/spack/spack/cmd/find.py
+++ b/lib/spack/spack/cmd/find.py
@@ -89,7 +89,7 @@ def find(parser, args):
                 format = "    %-{}s%s".format(width)
 
                 for abbrv, spec in zip(abbreviated, specs):
-                    print format % (abbrv, spec.package.prefix)
+                    print format % (abbrv, spec.prefix)
 
             elif args.full_specs:
                 for spec in specs:
diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index 816c945707b..9b31aad5fe1 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -29,6 +29,7 @@
 import shutil
 from contextlib import closing
 
+import llnl.util.tty as tty
 from llnl.util.filesystem import join_path, mkdirp
 
 import spack
@@ -163,6 +164,11 @@ def read_spec(self, path):
         if not spack.db.exists(spec.name):
             spec._normal = True
             spec._concrete = True
+        else:
+            spec.normalize()
+            if not spec.concrete:
+                tty.warn("Spec read from installed package is not concrete:",
+                         path, spec)
 
         return spec
 
diff --git a/lib/spack/spack/packages.py b/lib/spack/spack/packages.py
index 744ccae2d1b..ba997bf2691 100644
--- a/lib/spack/spack/packages.py
+++ b/lib/spack/spack/packages.py
@@ -115,7 +115,13 @@ def installed_package_specs(self):
         """Read installed package names straight from the install directory
            layout.
         """
-        return spack.install_layout.all_specs()
+        # Get specs from the directory layout but ensure that they're
+        # all normalized properly.
+        installed = []
+        for spec in spack.install_layout.all_specs():
+            spec.normalize()
+            installed.append(spec)
+        return installed
 
 
     @memoized
diff --git a/lib/spack/spack/test/install.py b/lib/spack/spack/test/install.py
index a92bd92289e..8047ab92e3e 100644
--- a/lib/spack/spack/test/install.py
+++ b/lib/spack/spack/test/install.py
@@ -25,15 +25,18 @@
 import os
 import unittest
 import shutil
+import tempfile
 from contextlib import closing
 
 from llnl.util.filesystem import *
 
 import spack
 from spack.stage import Stage
+from spack.directory_layout import SpecHashDirectoryLayout
 from spack.util.executable import which
 from spack.test.mock_packages_test import *
 
+
 dir_name = 'trivial-1.0'
 archive_name = 'trivial-1.0.tar.gz'
 install_test_package = 'trivial_install_test_package'
@@ -66,9 +69,16 @@ def setUp(self):
             tar = which('tar')
             tar('-czf', archive_name, dir_name)
 
-        # We use a fake pacakge, so skip the checksum.
+        # We use a fake package, so skip the checksum.
         spack.do_checksum = False
 
+        # Use a fake install directory to avoid conflicts bt/w
+        # installed pkgs and mock packages.
+        self.tmpdir = tempfile.mkdtemp()
+        self.orig_layout = spack.install_layout
+        spack.install_layout = SpecHashDirectoryLayout(self.tmpdir)
+
+
     def tearDown(self):
         super(InstallTest, self).tearDown()
 
@@ -78,6 +88,10 @@ def tearDown(self):
         # Turn checksumming back on
         spack.do_checksum = True
 
+        # restore spack's layout.
+        spack.install_layout = self.orig_layout
+        shutil.rmtree(self.tmpdir, ignore_errors=True)
+
 
     def test_install_and_uninstall(self):
         # Get a basic concrete spec for the trivial install package.

From 8ab793a3a67a6ef4573b0b2b1e68b293b6d9fd2e Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 10 Aug 2014 11:45:32 -0700
Subject: [PATCH 32/71] Add external package with pyqver2 tool

---
 lib/spack/external/__init__.py |  33 +++
 lib/spack/external/pyqver2.py  | 392 +++++++++++++++++++++++++++++++++
 2 files changed, 425 insertions(+)
 create mode 100644 lib/spack/external/__init__.py
 create mode 100755 lib/spack/external/pyqver2.py

diff --git a/lib/spack/external/__init__.py b/lib/spack/external/__init__.py
new file mode 100644
index 00000000000..1cc981930ad
--- /dev/null
+++ b/lib/spack/external/__init__.py
@@ -0,0 +1,33 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+"""
+This module contains external, potentially separately licensed,
+packages that are included in spack.
+
+So far:
+    argparse:    We include our own version to be Python 2.6 compatible.
+    pyqver2:     External script to query required python version of python source code.
+                 Used for ensuring 2.6 compatibility.
+"""
diff --git a/lib/spack/external/pyqver2.py b/lib/spack/external/pyqver2.py
new file mode 100755
index 00000000000..875f8837fb9
--- /dev/null
+++ b/lib/spack/external/pyqver2.py
@@ -0,0 +1,392 @@
+#!/usr/bin/env python
+#
+# pyqver2.py
+# by Greg Hewgill
+# https://github.com/ghewgill/pyqver
+#
+# This software is provided 'as-is', without any express or implied
+# warranty.  In no event will the author be held liable for any damages
+# arising from the use of this software.
+#
+# Permission is granted to anyone to use this software for any purpose,
+# including commercial applications, and to alter it and redistribute it
+# freely, subject to the following restrictions:
+#
+# 1. The origin of this software must not be misrepresented; you must not
+#    claim that you wrote the original software. If you use this software
+#    in a product, an acknowledgment in the product documentation would be
+#    appreciated but is not required.
+# 2. Altered source versions must be plainly marked as such, and must not be
+#    misrepresented as being the original software.
+# 3. This notice may not be removed or altered from any source distribution.
+#
+# Copyright (c) 2009-2013 Greg Hewgill http://hewgill.com
+#
+
+import compiler
+import platform
+import sys
+
+StandardModules = {
+    "__future__":       (2, 1),
+    "abc":              (2, 6),
+    "argparse":         (2, 7),
+    "ast":              (2, 6),
+    "atexit":           (2, 0),
+    "bz2":              (2, 3),
+    "cgitb":            (2, 2),
+    "collections":      (2, 4),
+    "contextlib":       (2, 5),
+    "cookielib":        (2, 4),
+    "cProfile":         (2, 5),
+    "csv":              (2, 3),
+    "ctypes":           (2, 5),
+    "datetime":         (2, 3),
+    "decimal":          (2, 4),
+    "difflib":          (2, 1),
+    "DocXMLRPCServer":  (2, 3),
+    "dummy_thread":     (2, 3),
+    "dummy_threading":  (2, 3),
+    "email":            (2, 2),
+    "fractions":        (2, 6),
+    "functools":        (2, 5),
+    "future_builtins":  (2, 6),
+    "hashlib":          (2, 5),
+    "heapq":            (2, 3),
+    "hmac":             (2, 2),
+    "hotshot":          (2, 2),
+    "HTMLParser":       (2, 2),
+    "importlib":        (2, 7),
+    "inspect":          (2, 1),
+    "io":               (2, 6),
+    "itertools":        (2, 3),
+    "json":             (2, 6),
+    "logging":          (2, 3),
+    "modulefinder":     (2, 3),
+    "msilib":           (2, 5),
+    "multiprocessing":  (2, 6),
+    "netrc":            (1, 5, 2),
+    "numbers":          (2, 6),
+    "optparse":         (2, 3),
+    "ossaudiodev":      (2, 3),
+    "pickletools":      (2, 3),
+    "pkgutil":          (2, 3),
+    "platform":         (2, 3),
+    "pydoc":            (2, 1),
+    "runpy":            (2, 5),
+    "sets":             (2, 3),
+    "shlex":            (1, 5, 2),
+    "SimpleXMLRPCServer": (2, 2),
+    "spwd":             (2, 5),
+    "sqlite3":          (2, 5),
+    "ssl":              (2, 6),
+    "stringprep":       (2, 3),
+    "subprocess":       (2, 4),
+    "sysconfig":        (2, 7),
+    "tarfile":          (2, 3),
+    "textwrap":         (2, 3),
+    "timeit":           (2, 3),
+    "unittest":         (2, 1),
+    "uuid":             (2, 5),
+    "warnings":         (2, 1),
+    "weakref":          (2, 1),
+    "winsound":         (1, 5, 2),
+    "wsgiref":          (2, 5),
+    "xml.dom":          (2, 0),
+    "xml.dom.minidom":  (2, 0),
+    "xml.dom.pulldom":  (2, 0),
+    "xml.etree.ElementTree": (2, 5),
+    "xml.parsers.expat":(2, 0),
+    "xml.sax":          (2, 0),
+    "xml.sax.handler":  (2, 0),
+    "xml.sax.saxutils": (2, 0),
+    "xml.sax.xmlreader":(2, 0),
+    "xmlrpclib":        (2, 2),
+    "zipfile":          (1, 6),
+    "zipimport":        (2, 3),
+    "_ast":             (2, 5),
+    "_winreg":          (2, 0),
+}
+
+Functions = {
+    "all":                      (2, 5),
+    "any":                      (2, 5),
+    "collections.Counter":      (2, 7),
+    "collections.defaultdict":  (2, 5),
+    "collections.OrderedDict":  (2, 7),
+    "enumerate":                (2, 3),
+    "frozenset":                (2, 4),
+    "itertools.compress":       (2, 7),
+    "math.erf":                 (2, 7),
+    "math.erfc":                (2, 7),
+    "math.expm1":               (2, 7),
+    "math.gamma":               (2, 7),
+    "math.lgamma":              (2, 7),
+    "memoryview":               (2, 7),
+    "next":                     (2, 6),
+    "os.getresgid":             (2, 7),
+    "os.getresuid":             (2, 7),
+    "os.initgroups":            (2, 7),
+    "os.setresgid":             (2, 7),
+    "os.setresuid":             (2, 7),
+    "reversed":                 (2, 4),
+    "set":                      (2, 4),
+    "subprocess.check_call":    (2, 5),
+    "subprocess.check_output":  (2, 7),
+    "sum":                      (2, 3),
+    "symtable.is_declared_global": (2, 7),
+    "weakref.WeakSet":          (2, 7),
+}
+
+Identifiers = {
+    "False":        (2, 2),
+    "True":         (2, 2),
+}
+
+def uniq(a):
+    if len(a) == 0:
+        return []
+    else:
+        return [a[0]] + uniq([x for x in a if x != a[0]])
+
+class NodeChecker(object):
+    def __init__(self):
+        self.vers = dict()
+        self.vers[(2,0)] = []
+    def add(self, node, ver, msg):
+        if ver not in self.vers:
+            self.vers[ver] = []
+        self.vers[ver].append((node.lineno, msg))
+    def default(self, node):
+        for child in node.getChildNodes():
+            self.visit(child)
+    def visitCallFunc(self, node):
+        def rollup(n):
+            if isinstance(n, compiler.ast.Name):
+                return n.name
+            elif isinstance(n, compiler.ast.Getattr):
+                r = rollup(n.expr)
+                if r:
+                    return r + "." + n.attrname
+        name = rollup(node.node)
+        if name:
+            v = Functions.get(name)
+            if v is not None:
+                self.add(node, v, name)
+        self.default(node)
+    def visitClass(self, node):
+        if node.bases:
+            self.add(node, (2,2), "new-style class")
+        if node.decorators:
+            self.add(node, (2,6), "class decorator")
+        self.default(node)
+    def visitDictComp(self, node):
+        self.add(node, (2,7), "dictionary comprehension")
+        self.default(node)
+    def visitFloorDiv(self, node):
+        self.add(node, (2,2), "// operator")
+        self.default(node)
+    def visitFrom(self, node):
+        v = StandardModules.get(node.modname)
+        if v is not None:
+            self.add(node, v, node.modname)
+        for n in node.names:
+            name = node.modname + "." + n[0]
+            v = Functions.get(name)
+            if v is not None:
+                self.add(node, v, name)
+    def visitFunction(self, node):
+        if node.decorators:
+            self.add(node, (2,4), "function decorator")
+        self.default(node)
+    def visitGenExpr(self, node):
+        self.add(node, (2,4), "generator expression")
+        self.default(node)
+    def visitGetattr(self, node):
+        if (isinstance(node.expr, compiler.ast.Const)
+            and isinstance(node.expr.value, str)
+            and node.attrname == "format"):
+            self.add(node, (2,6), "string literal .format()")
+        self.default(node)
+    def visitIfExp(self, node):
+        self.add(node, (2,5), "inline if expression")
+        self.default(node)
+    def visitImport(self, node):
+        for n in node.names:
+            v = StandardModules.get(n[0])
+            if v is not None:
+                self.add(node, v, n[0])
+        self.default(node)
+    def visitName(self, node):
+        v = Identifiers.get(node.name)
+        if v is not None:
+            self.add(node, v, node.name)
+        self.default(node)
+    def visitSet(self, node):
+        self.add(node, (2,7), "set literal")
+        self.default(node)
+    def visitSetComp(self, node):
+        self.add(node, (2,7), "set comprehension")
+        self.default(node)
+    def visitTryFinally(self, node):
+        # try/finally with a suite generates a Stmt node as the body,
+        # but try/except/finally generates a TryExcept as the body
+        if isinstance(node.body, compiler.ast.TryExcept):
+            self.add(node, (2,5), "try/except/finally")
+        self.default(node)
+    def visitWith(self, node):
+        if isinstance(node.body, compiler.ast.With):
+            self.add(node, (2,7), "with statement with multiple contexts")
+        else:
+            self.add(node, (2,5), "with statement")
+        self.default(node)
+    def visitYield(self, node):
+        self.add(node, (2,2), "yield expression")
+        self.default(node)
+
+def get_versions(source):
+    """Return information about the Python versions required for specific features.
+
+    The return value is a dictionary with keys as a version number as a tuple
+    (for example Python 2.6 is (2,6)) and the value are a list of features that
+    require the indicated Python version.
+    """
+    tree = compiler.parse(source)
+    checker = compiler.walk(tree, NodeChecker())
+    return checker.vers
+
+def v27(source):
+    if sys.version_info >= (2, 7):
+        return qver(source)
+    else:
+        print >>sys.stderr, "Not all features tested, run --test with Python 2.7"
+        return (2, 7)
+
+def qver(source):
+    """Return the minimum Python version required to run a particular bit of code.
+
+    >>> qver('print "hello world"')
+    (2, 0)
+    >>> qver('class test(object): pass')
+    (2, 2)
+    >>> qver('yield 1')
+    (2, 2)
+    >>> qver('a // b')
+    (2, 2)
+    >>> qver('True')
+    (2, 2)
+    >>> qver('enumerate(a)')
+    (2, 3)
+    >>> qver('total = sum')
+    (2, 0)
+    >>> qver('sum(a)')
+    (2, 3)
+    >>> qver('(x*x for x in range(5))')
+    (2, 4)
+    >>> qver('class C:\\n @classmethod\\n def m(): pass')
+    (2, 4)
+    >>> qver('y if x else z')
+    (2, 5)
+    >>> qver('import hashlib')
+    (2, 5)
+    >>> qver('from hashlib import md5')
+    (2, 5)
+    >>> qver('import xml.etree.ElementTree')
+    (2, 5)
+    >>> qver('try:\\n try: pass;\\n except: pass;\\nfinally: pass')
+    (2, 0)
+    >>> qver('try: pass;\\nexcept: pass;\\nfinally: pass')
+    (2, 5)
+    >>> qver('from __future__ import with_statement\\nwith x: pass')
+    (2, 5)
+    >>> qver('collections.defaultdict(list)')
+    (2, 5)
+    >>> qver('from collections import defaultdict')
+    (2, 5)
+    >>> qver('"{0}".format(0)')
+    (2, 6)
+    >>> qver('memoryview(x)')
+    (2, 7)
+    >>> v27('{1, 2, 3}')
+    (2, 7)
+    >>> v27('{x for x in s}')
+    (2, 7)
+    >>> v27('{x: y for x in s}')
+    (2, 7)
+    >>> qver('from __future__ import with_statement\\nwith x:\\n with y: pass')
+    (2, 5)
+    >>> v27('from __future__ import with_statement\\nwith x, y: pass')
+    (2, 7)
+    >>> qver('@decorator\\ndef f(): pass')
+    (2, 4)
+    >>> qver('@decorator\\nclass test:\\n pass')
+    (2, 6)
+
+    #>>> qver('0o0')
+    #(2, 6)
+    #>>> qver('@foo\\nclass C: pass')
+    #(2, 6)
+    """
+    return max(get_versions(source).keys())
+
+
+if __name__ == '__main__':
+
+    Verbose = False
+    MinVersion = (2, 3)
+    Lint = False
+
+    files = []
+    i = 1
+    while i < len(sys.argv):
+        a = sys.argv[i]
+        if a == "--test":
+            import doctest
+            doctest.testmod()
+            sys.exit(0)
+        if a == "-v" or a == "--verbose":
+            Verbose = True
+        elif a == "-l" or a == "--lint":
+            Lint = True
+        elif a == "-m" or a == "--min-version":
+            i += 1
+            MinVersion = tuple(map(int, sys.argv[i].split(".")))
+        else:
+            files.append(a)
+        i += 1
+
+    if not files:
+        print >>sys.stderr, """Usage: %s [options] source ...
+
+        Report minimum Python version required to run given source files.
+
+        -m x.y or --min-version x.y (default 2.3)
+            report version triggers at or above version x.y in verbose mode
+        -v or --verbose
+            print more detailed report of version triggers for each version
+    """ % sys.argv[0]
+        sys.exit(1)
+
+    for fn in files:
+        try:
+            f = open(fn)
+            source = f.read()
+            f.close()
+            ver = get_versions(source)
+            if Verbose:
+                print fn
+                for v in sorted([k for k in ver.keys() if k >= MinVersion], reverse=True):
+                    reasons = [x for x in uniq(ver[v]) if x]
+                    if reasons:
+                        # each reason is (lineno, message)
+                        print "\t%s\t%s" % (".".join(map(str, v)), ", ".join([x[1] for x in reasons]))
+            elif Lint:
+                for v in sorted([k for k in ver.keys() if k >= MinVersion], reverse=True):
+                    reasons = [x for x in uniq(ver[v]) if x]
+                    for r in reasons:
+                        # each reason is (lineno, message)
+                        print "%s:%s: %s %s" % (fn, r[0], ".".join(map(str, v)), r[1])
+            else:
+                print "%s\t%s" % (".".join(map(str, max(ver.keys()))), fn)
+        except SyntaxError, x:
+            print "%s: syntax error compiling with Python %s: %s" % (fn, platform.python_version(), x)

From 17895bd6fda34ec10b46a339bf2210fee5a17723 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 10 Aug 2014 11:46:14 -0700
Subject: [PATCH 33/71] Add a test case to ensure that Spack is v2.6 compliant.

---
 lib/spack/spack/test/__init__.py       |  3 +-
 lib/spack/spack/test/python_version.py | 96 ++++++++++++++++++++++++++
 2 files changed, 98 insertions(+), 1 deletion(-)
 create mode 100644 lib/spack/spack/test/python_version.py

diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py
index c2dfc51aa3f..4479c45d770 100644
--- a/lib/spack/spack/test/__init__.py
+++ b/lib/spack/spack/test/__init__.py
@@ -46,7 +46,8 @@
               'install',
               'package_sanity',
               'config',
-              'directory_layout']
+              'directory_layout',
+              'python_version']
 
 
 def list_tests():
diff --git a/lib/spack/spack/test/python_version.py b/lib/spack/spack/test/python_version.py
new file mode 100644
index 00000000000..f814df32261
--- /dev/null
+++ b/lib/spack/spack/test/python_version.py
@@ -0,0 +1,96 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+"""
+This test ensures that all Spack files are Python version 2.6 or less.
+
+Spack was originally 2.7, but enough systems in 2014 are still using
+2.6 on their frontend nodes that we need 2.6 to get adopted.
+"""
+import unittest
+import os
+import re
+from contextlib import closing
+
+import llnl.util.tty as tty
+
+from external import pyqver2
+import spack
+
+spack_max_version = (2,6)
+
+class PythonVersionTest(unittest.TestCase):
+
+    def spack_python_files(self):
+        # first file is the spack script.
+        yield spack.spack_file
+
+        # Next files are all the source files and package files.
+        search_paths = [spack.lib_path, spack.var_path]
+
+        # Iterate through the whole spack source tree.
+        for path in search_paths:
+            for root, dirnames, filenames in os.walk(path):
+                for filename in filenames:
+                    if re.match(r'^[^.#].*\.py$', filename):
+                        yield os.path.join(root, filename)
+
+
+    def test_python_versions(self):
+        # dict version -> filename -> reasons
+        all_issues = {}
+
+        for fn in self.spack_python_files():
+            with closing(open(fn)) as pyfile:
+                versions = pyqver2.get_versions(pyfile.read())
+                for ver, reasons in versions.items():
+                    if ver > spack_max_version:
+                        if not ver in all_issues:
+                            all_issues[ver] = {}
+                        all_issues[ver][fn] = reasons
+
+        if all_issues:
+            tty.error("Spack must run on Python version %d.%d"
+                      % spack_max_version)
+
+        for v in sorted(all_issues.keys(), reverse=True):
+            msgs = []
+            for fn in sorted(all_issues[v].keys()):
+                short_fn = fn
+                if fn.startswith(spack.prefix):
+                    short_fn = fn[len(spack.prefix):]
+
+                reasons = [r for r in set(all_issues[v][fn]) if r]
+                for r in reasons:
+                    msgs.append(("%s:%s" % ('spack' + short_fn, r[0]), r[1]))
+
+            tty.error("These files require version %d.%d:" % v)
+            maxlen = max(len(f) for f, prob in msgs)
+            fmt = "%%-%ds%%s" % (maxlen+3)
+            print fmt % ('File', 'Reason')
+            print fmt % ('-' * (maxlen), '-' * 20)
+            for msg in msgs:
+                print fmt % msg
+
+        self.assertTrue(len(all_issues) == 0)

From 7714d08e2e4b1c7accd6113618651b42bdc942c1 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 10 Aug 2014 11:48:07 -0700
Subject: [PATCH 34/71] Remvoe dependence on v2.7 argparse by including
 argparse.

---
 bin/spack                         |    2 +-
 lib/spack/external/argparse.py    | 2382 +++++++++++++++++++++++++++++
 lib/spack/spack/cmd/checksum.py   |    2 +-
 lib/spack/spack/cmd/clean.py      |    2 +-
 lib/spack/spack/cmd/compiler.py   |    2 +-
 lib/spack/spack/cmd/config.py     |    2 +-
 lib/spack/spack/cmd/dependents.py |    2 +-
 lib/spack/spack/cmd/dotkit.py     |    2 +-
 lib/spack/spack/cmd/fetch.py      |    2 +-
 lib/spack/spack/cmd/find.py       |    2 +-
 lib/spack/spack/cmd/install.py    |    2 +-
 lib/spack/spack/cmd/mirror.py     |    2 +-
 lib/spack/spack/cmd/patch.py      |    2 +-
 lib/spack/spack/cmd/providers.py  |    2 +-
 lib/spack/spack/cmd/python.py     |    2 +-
 lib/spack/spack/cmd/spec.py       |    2 +-
 lib/spack/spack/cmd/stage.py      |    2 +-
 lib/spack/spack/cmd/uninstall.py  |    2 +-
 lib/spack/spack/cmd/unuse.py      |    2 +-
 lib/spack/spack/cmd/use.py        |    2 +-
 lib/spack/spack/relations.py      |    1 -
 21 files changed, 2401 insertions(+), 20 deletions(-)
 create mode 100644 lib/spack/external/argparse.py

diff --git a/bin/spack b/bin/spack
index c63178b1913..0af8d62b5e2 100755
--- a/bin/spack
+++ b/bin/spack
@@ -28,7 +28,6 @@ if not sys.version_info[:2] >= (2,7):
     sys.exit("Spack requires Python 2.7.  Version was %s." % sys.version_info)
 
 import os
-import argparse
 
 # Find spack's location and its prefix.
 SPACK_FILE = os.path.realpath(os.path.expanduser(__file__))
@@ -51,6 +50,7 @@ del SPACK_FILE, SPACK_PREFIX, SPACK_LIB_PATH
 import llnl.util.tty as tty
 import spack
 from spack.error import SpackError
+from external import argparse
 
 # Command parsing
 parser = argparse.ArgumentParser(
diff --git a/lib/spack/external/argparse.py b/lib/spack/external/argparse.py
new file mode 100644
index 00000000000..c8dfdd3bed2
--- /dev/null
+++ b/lib/spack/external/argparse.py
@@ -0,0 +1,2382 @@
+# argparse is (c) 2006-2009 Steven J. Bethard <steven.bethard@gmail.com>.
+#
+# The argparse module was contributed to Python as of Python 2.7 and thus
+# was licensed under the Python license. Same license applies to all files in
+# the argparse package project.
+#
+# For details about the Python License, please see doc/Python-License.txt.
+#
+# History
+# -------
+#
+# Before (and including) argparse 1.1, the argparse package was licensed under
+# Apache License v2.0.
+#
+# After argparse 1.1, all project files from the argparse project were deleted
+# due to license compatibility issues between Apache License 2.0 and GNU GPL v2.
+#
+# The project repository then had a clean start with some files taken from
+# Python 2.7.1, so definitely all files are under Python License now.
+#
+# Author: Steven J. Bethard <steven.bethard@gmail.com>.
+#
+"""Command-line parsing library
+
+This module is an optparse-inspired command-line parsing library that:
+
+    - handles both optional and positional arguments
+    - produces highly informative usage messages
+    - supports parsers that dispatch to sub-parsers
+
+The following is a simple usage example that sums integers from the
+command-line and writes the result to a file::
+
+    parser = argparse.ArgumentParser(
+        description='sum the integers at the command line')
+    parser.add_argument(
+        'integers', metavar='int', nargs='+', type=int,
+        help='an integer to be summed')
+    parser.add_argument(
+        '--log', default=sys.stdout, type=argparse.FileType('w'),
+        help='the file where the sum should be written')
+    args = parser.parse_args()
+    args.log.write('%s' % sum(args.integers))
+    args.log.close()
+
+The module contains the following public classes:
+
+    - ArgumentParser -- The main entry point for command-line parsing. As the
+        example above shows, the add_argument() method is used to populate
+        the parser with actions for optional and positional arguments. Then
+        the parse_args() method is invoked to convert the args at the
+        command-line into an object with attributes.
+
+    - ArgumentError -- The exception raised by ArgumentParser objects when
+        there are errors with the parser's actions. Errors raised while
+        parsing the command-line are caught by ArgumentParser and emitted
+        as command-line messages.
+
+    - FileType -- A factory for defining types of files to be created. As the
+        example above shows, instances of FileType are typically passed as
+        the type= argument of add_argument() calls.
+
+    - Action -- The base class for parser actions. Typically actions are
+        selected by passing strings like 'store_true' or 'append_const' to
+        the action= argument of add_argument(). However, for greater
+        customization of ArgumentParser actions, subclasses of Action may
+        be defined and passed as the action= argument.
+
+    - HelpFormatter, RawDescriptionHelpFormatter, RawTextHelpFormatter,
+        ArgumentDefaultsHelpFormatter -- Formatter classes which
+        may be passed as the formatter_class= argument to the
+        ArgumentParser constructor. HelpFormatter is the default,
+        RawDescriptionHelpFormatter and RawTextHelpFormatter tell the parser
+        not to change the formatting for help text, and
+        ArgumentDefaultsHelpFormatter adds information about argument defaults
+        to the help.
+
+All other classes in this module are considered implementation details.
+(Also note that HelpFormatter and RawDescriptionHelpFormatter are only
+considered public as object names -- the API of the formatter objects is
+still considered an implementation detail.)
+"""
+
+__version__ = '1.2.1'
+__all__ = [
+    'ArgumentParser',
+    'ArgumentError',
+    'ArgumentTypeError',
+    'FileType',
+    'HelpFormatter',
+    'ArgumentDefaultsHelpFormatter',
+    'RawDescriptionHelpFormatter',
+    'RawTextHelpFormatter',
+    'Namespace',
+    'Action',
+    'ONE_OR_MORE',
+    'OPTIONAL',
+    'PARSER',
+    'REMAINDER',
+    'SUPPRESS',
+    'ZERO_OR_MORE',
+]
+
+
+import copy as _copy
+import os as _os
+import re as _re
+import sys as _sys
+import textwrap as _textwrap
+
+from gettext import gettext as _
+
+try:
+    set
+except NameError:
+    # for python < 2.4 compatibility (sets module is there since 2.3):
+    from sets import Set as set
+
+try:
+    basestring
+except NameError:
+    basestring = str
+
+try:
+    sorted
+except NameError:
+    # for python < 2.4 compatibility:
+    def sorted(iterable, reverse=False):
+        result = list(iterable)
+        result.sort()
+        if reverse:
+            result.reverse()
+        return result
+
+
+def _callable(obj):
+    return hasattr(obj, '__call__') or hasattr(obj, '__bases__')
+
+
+SUPPRESS = '==SUPPRESS=='
+
+OPTIONAL = '?'
+ZERO_OR_MORE = '*'
+ONE_OR_MORE = '+'
+PARSER = 'A...'
+REMAINDER = '...'
+_UNRECOGNIZED_ARGS_ATTR = '_unrecognized_args'
+
+# =============================
+# Utility functions and classes
+# =============================
+
+class _AttributeHolder(object):
+    """Abstract base class that provides __repr__.
+
+    The __repr__ method returns a string in the format::
+        ClassName(attr=name, attr=name, ...)
+    The attributes are determined either by a class-level attribute,
+    '_kwarg_names', or by inspecting the instance __dict__.
+    """
+
+    def __repr__(self):
+        type_name = type(self).__name__
+        arg_strings = []
+        for arg in self._get_args():
+            arg_strings.append(repr(arg))
+        for name, value in self._get_kwargs():
+            arg_strings.append('%s=%r' % (name, value))
+        return '%s(%s)' % (type_name, ', '.join(arg_strings))
+
+    def _get_kwargs(self):
+        return sorted(self.__dict__.items())
+
+    def _get_args(self):
+        return []
+
+
+def _ensure_value(namespace, name, value):
+    if getattr(namespace, name, None) is None:
+        setattr(namespace, name, value)
+    return getattr(namespace, name)
+
+
+# ===============
+# Formatting Help
+# ===============
+
+class HelpFormatter(object):
+    """Formatter for generating usage messages and argument help strings.
+
+    Only the name of this class is considered a public API. All the methods
+    provided by the class are considered an implementation detail.
+    """
+
+    def __init__(self,
+                 prog,
+                 indent_increment=2,
+                 max_help_position=24,
+                 width=None):
+
+        # default setting for width
+        if width is None:
+            try:
+                width = int(_os.environ['COLUMNS'])
+            except (KeyError, ValueError):
+                width = 80
+            width -= 2
+
+        self._prog = prog
+        self._indent_increment = indent_increment
+        self._max_help_position = max_help_position
+        self._width = width
+
+        self._current_indent = 0
+        self._level = 0
+        self._action_max_length = 0
+
+        self._root_section = self._Section(self, None)
+        self._current_section = self._root_section
+
+        self._whitespace_matcher = _re.compile(r'\s+')
+        self._long_break_matcher = _re.compile(r'\n\n\n+')
+
+    # ===============================
+    # Section and indentation methods
+    # ===============================
+    def _indent(self):
+        self._current_indent += self._indent_increment
+        self._level += 1
+
+    def _dedent(self):
+        self._current_indent -= self._indent_increment
+        assert self._current_indent >= 0, 'Indent decreased below 0.'
+        self._level -= 1
+
+    class _Section(object):
+
+        def __init__(self, formatter, parent, heading=None):
+            self.formatter = formatter
+            self.parent = parent
+            self.heading = heading
+            self.items = []
+
+        def format_help(self):
+            # format the indented section
+            if self.parent is not None:
+                self.formatter._indent()
+            join = self.formatter._join_parts
+            for func, args in self.items:
+                func(*args)
+            item_help = join([func(*args) for func, args in self.items])
+            if self.parent is not None:
+                self.formatter._dedent()
+
+            # return nothing if the section was empty
+            if not item_help:
+                return ''
+
+            # add the heading if the section was non-empty
+            if self.heading is not SUPPRESS and self.heading is not None:
+                current_indent = self.formatter._current_indent
+                heading = '%*s%s:\n' % (current_indent, '', self.heading)
+            else:
+                heading = ''
+
+            # join the section-initial newline, the heading and the help
+            return join(['\n', heading, item_help, '\n'])
+
+    def _add_item(self, func, args):
+        self._current_section.items.append((func, args))
+
+    # ========================
+    # Message building methods
+    # ========================
+    def start_section(self, heading):
+        self._indent()
+        section = self._Section(self, self._current_section, heading)
+        self._add_item(section.format_help, [])
+        self._current_section = section
+
+    def end_section(self):
+        self._current_section = self._current_section.parent
+        self._dedent()
+
+    def add_text(self, text):
+        if text is not SUPPRESS and text is not None:
+            self._add_item(self._format_text, [text])
+
+    def add_usage(self, usage, actions, groups, prefix=None):
+        if usage is not SUPPRESS:
+            args = usage, actions, groups, prefix
+            self._add_item(self._format_usage, args)
+
+    def add_argument(self, action):
+        if action.help is not SUPPRESS:
+
+            # find all invocations
+            get_invocation = self._format_action_invocation
+            invocations = [get_invocation(action)]
+            for subaction in self._iter_indented_subactions(action):
+                invocations.append(get_invocation(subaction))
+
+            # update the maximum item length
+            invocation_length = max([len(s) for s in invocations])
+            action_length = invocation_length + self._current_indent
+            self._action_max_length = max(self._action_max_length,
+                                          action_length)
+
+            # add the item to the list
+            self._add_item(self._format_action, [action])
+
+    def add_arguments(self, actions):
+        for action in actions:
+            self.add_argument(action)
+
+    # =======================
+    # Help-formatting methods
+    # =======================
+    def format_help(self):
+        help = self._root_section.format_help()
+        if help:
+            help = self._long_break_matcher.sub('\n\n', help)
+            help = help.strip('\n') + '\n'
+        return help
+
+    def _join_parts(self, part_strings):
+        return ''.join([part
+                        for part in part_strings
+                        if part and part is not SUPPRESS])
+
+    def _format_usage(self, usage, actions, groups, prefix):
+        if prefix is None:
+            prefix = _('usage: ')
+
+        # if usage is specified, use that
+        if usage is not None:
+            usage = usage % dict(prog=self._prog)
+
+        # if no optionals or positionals are available, usage is just prog
+        elif usage is None and not actions:
+            usage = '%(prog)s' % dict(prog=self._prog)
+
+        # if optionals and positionals are available, calculate usage
+        elif usage is None:
+            prog = '%(prog)s' % dict(prog=self._prog)
+
+            # split optionals from positionals
+            optionals = []
+            positionals = []
+            for action in actions:
+                if action.option_strings:
+                    optionals.append(action)
+                else:
+                    positionals.append(action)
+
+            # build full usage string
+            format = self._format_actions_usage
+            action_usage = format(optionals + positionals, groups)
+            usage = ' '.join([s for s in [prog, action_usage] if s])
+
+            # wrap the usage parts if it's too long
+            text_width = self._width - self._current_indent
+            if len(prefix) + len(usage) > text_width:
+
+                # break usage into wrappable parts
+                part_regexp = r'\(.*?\)+|\[.*?\]+|\S+'
+                opt_usage = format(optionals, groups)
+                pos_usage = format(positionals, groups)
+                opt_parts = _re.findall(part_regexp, opt_usage)
+                pos_parts = _re.findall(part_regexp, pos_usage)
+                assert ' '.join(opt_parts) == opt_usage
+                assert ' '.join(pos_parts) == pos_usage
+
+                # helper for wrapping lines
+                def get_lines(parts, indent, prefix=None):
+                    lines = []
+                    line = []
+                    if prefix is not None:
+                        line_len = len(prefix) - 1
+                    else:
+                        line_len = len(indent) - 1
+                    for part in parts:
+                        if line_len + 1 + len(part) > text_width:
+                            lines.append(indent + ' '.join(line))
+                            line = []
+                            line_len = len(indent) - 1
+                        line.append(part)
+                        line_len += len(part) + 1
+                    if line:
+                        lines.append(indent + ' '.join(line))
+                    if prefix is not None:
+                        lines[0] = lines[0][len(indent):]
+                    return lines
+
+                # if prog is short, follow it with optionals or positionals
+                if len(prefix) + len(prog) <= 0.75 * text_width:
+                    indent = ' ' * (len(prefix) + len(prog) + 1)
+                    if opt_parts:
+                        lines = get_lines([prog] + opt_parts, indent, prefix)
+                        lines.extend(get_lines(pos_parts, indent))
+                    elif pos_parts:
+                        lines = get_lines([prog] + pos_parts, indent, prefix)
+                    else:
+                        lines = [prog]
+
+                # if prog is long, put it on its own line
+                else:
+                    indent = ' ' * len(prefix)
+                    parts = opt_parts + pos_parts
+                    lines = get_lines(parts, indent)
+                    if len(lines) > 1:
+                        lines = []
+                        lines.extend(get_lines(opt_parts, indent))
+                        lines.extend(get_lines(pos_parts, indent))
+                    lines = [prog] + lines
+
+                # join lines into usage
+                usage = '\n'.join(lines)
+
+        # prefix with 'usage:'
+        return '%s%s\n\n' % (prefix, usage)
+
+    def _format_actions_usage(self, actions, groups):
+        # find group indices and identify actions in groups
+        group_actions = set()
+        inserts = {}
+        for group in groups:
+            try:
+                start = actions.index(group._group_actions[0])
+            except ValueError:
+                continue
+            else:
+                end = start + len(group._group_actions)
+                if actions[start:end] == group._group_actions:
+                    for action in group._group_actions:
+                        group_actions.add(action)
+                    if not group.required:
+                        if start in inserts:
+                            inserts[start] += ' ['
+                        else:
+                            inserts[start] = '['
+                        inserts[end] = ']'
+                    else:
+                        if start in inserts:
+                            inserts[start] += ' ('
+                        else:
+                            inserts[start] = '('
+                        inserts[end] = ')'
+                    for i in range(start + 1, end):
+                        inserts[i] = '|'
+
+        # collect all actions format strings
+        parts = []
+        for i, action in enumerate(actions):
+
+            # suppressed arguments are marked with None
+            # remove | separators for suppressed arguments
+            if action.help is SUPPRESS:
+                parts.append(None)
+                if inserts.get(i) == '|':
+                    inserts.pop(i)
+                elif inserts.get(i + 1) == '|':
+                    inserts.pop(i + 1)
+
+            # produce all arg strings
+            elif not action.option_strings:
+                part = self._format_args(action, action.dest)
+
+                # if it's in a group, strip the outer []
+                if action in group_actions:
+                    if part[0] == '[' and part[-1] == ']':
+                        part = part[1:-1]
+
+                # add the action string to the list
+                parts.append(part)
+
+            # produce the first way to invoke the option in brackets
+            else:
+                option_string = action.option_strings[0]
+
+                # if the Optional doesn't take a value, format is:
+                #    -s or --long
+                if action.nargs == 0:
+                    part = '%s' % option_string
+
+                # if the Optional takes a value, format is:
+                #    -s ARGS or --long ARGS
+                else:
+                    default = action.dest.upper()
+                    args_string = self._format_args(action, default)
+                    part = '%s %s' % (option_string, args_string)
+
+                # make it look optional if it's not required or in a group
+                if not action.required and action not in group_actions:
+                    part = '[%s]' % part
+
+                # add the action string to the list
+                parts.append(part)
+
+        # insert things at the necessary indices
+        for i in sorted(inserts, reverse=True):
+            parts[i:i] = [inserts[i]]
+
+        # join all the action items with spaces
+        text = ' '.join([item for item in parts if item is not None])
+
+        # clean up separators for mutually exclusive groups
+        open = r'[\[(]'
+        close = r'[\])]'
+        text = _re.sub(r'(%s) ' % open, r'\1', text)
+        text = _re.sub(r' (%s)' % close, r'\1', text)
+        text = _re.sub(r'%s *%s' % (open, close), r'', text)
+        text = _re.sub(r'\(([^|]*)\)', r'\1', text)
+        text = text.strip()
+
+        # return the text
+        return text
+
+    def _format_text(self, text):
+        if '%(prog)' in text:
+            text = text % dict(prog=self._prog)
+        text_width = self._width - self._current_indent
+        indent = ' ' * self._current_indent
+        return self._fill_text(text, text_width, indent) + '\n\n'
+
+    def _format_action(self, action):
+        # determine the required width and the entry label
+        help_position = min(self._action_max_length + 2,
+                            self._max_help_position)
+        help_width = self._width - help_position
+        action_width = help_position - self._current_indent - 2
+        action_header = self._format_action_invocation(action)
+
+        # ho nelp; start on same line and add a final newline
+        if not action.help:
+            tup = self._current_indent, '', action_header
+            action_header = '%*s%s\n' % tup
+
+        # short action name; start on the same line and pad two spaces
+        elif len(action_header) <= action_width:
+            tup = self._current_indent, '', action_width, action_header
+            action_header = '%*s%-*s  ' % tup
+            indent_first = 0
+
+        # long action name; start on the next line
+        else:
+            tup = self._current_indent, '', action_header
+            action_header = '%*s%s\n' % tup
+            indent_first = help_position
+
+        # collect the pieces of the action help
+        parts = [action_header]
+
+        # if there was help for the action, add lines of help text
+        if action.help:
+            help_text = self._expand_help(action)
+            help_lines = self._split_lines(help_text, help_width)
+            parts.append('%*s%s\n' % (indent_first, '', help_lines[0]))
+            for line in help_lines[1:]:
+                parts.append('%*s%s\n' % (help_position, '', line))
+
+        # or add a newline if the description doesn't end with one
+        elif not action_header.endswith('\n'):
+            parts.append('\n')
+
+        # if there are any sub-actions, add their help as well
+        for subaction in self._iter_indented_subactions(action):
+            parts.append(self._format_action(subaction))
+
+        # return a single string
+        return self._join_parts(parts)
+
+    def _format_action_invocation(self, action):
+        if not action.option_strings:
+            metavar, = self._metavar_formatter(action, action.dest)(1)
+            return metavar
+
+        else:
+            parts = []
+
+            # if the Optional doesn't take a value, format is:
+            #    -s, --long
+            if action.nargs == 0:
+                parts.extend(action.option_strings)
+
+            # if the Optional takes a value, format is:
+            #    -s ARGS, --long ARGS
+            else:
+                default = action.dest.upper()
+                args_string = self._format_args(action, default)
+                for option_string in action.option_strings:
+                    parts.append('%s %s' % (option_string, args_string))
+
+            return ', '.join(parts)
+
+    def _metavar_formatter(self, action, default_metavar):
+        if action.metavar is not None:
+            result = action.metavar
+        elif action.choices is not None:
+            choice_strs = [str(choice) for choice in action.choices]
+            result = '{%s}' % ','.join(choice_strs)
+        else:
+            result = default_metavar
+
+        def format(tuple_size):
+            if isinstance(result, tuple):
+                return result
+            else:
+                return (result, ) * tuple_size
+        return format
+
+    def _format_args(self, action, default_metavar):
+        get_metavar = self._metavar_formatter(action, default_metavar)
+        if action.nargs is None:
+            result = '%s' % get_metavar(1)
+        elif action.nargs == OPTIONAL:
+            result = '[%s]' % get_metavar(1)
+        elif action.nargs == ZERO_OR_MORE:
+            result = '[%s [%s ...]]' % get_metavar(2)
+        elif action.nargs == ONE_OR_MORE:
+            result = '%s [%s ...]' % get_metavar(2)
+        elif action.nargs == REMAINDER:
+            result = '...'
+        elif action.nargs == PARSER:
+            result = '%s ...' % get_metavar(1)
+        else:
+            formats = ['%s' for _ in range(action.nargs)]
+            result = ' '.join(formats) % get_metavar(action.nargs)
+        return result
+
+    def _expand_help(self, action):
+        params = dict(vars(action), prog=self._prog)
+        for name in list(params):
+            if params[name] is SUPPRESS:
+                del params[name]
+        for name in list(params):
+            if hasattr(params[name], '__name__'):
+                params[name] = params[name].__name__
+        if params.get('choices') is not None:
+            choices_str = ', '.join([str(c) for c in params['choices']])
+            params['choices'] = choices_str
+        return self._get_help_string(action) % params
+
+    def _iter_indented_subactions(self, action):
+        try:
+            get_subactions = action._get_subactions
+        except AttributeError:
+            pass
+        else:
+            self._indent()
+            for subaction in get_subactions():
+                yield subaction
+            self._dedent()
+
+    def _split_lines(self, text, width):
+        text = self._whitespace_matcher.sub(' ', text).strip()
+        return _textwrap.wrap(text, width)
+
+    def _fill_text(self, text, width, indent):
+        text = self._whitespace_matcher.sub(' ', text).strip()
+        return _textwrap.fill(text, width, initial_indent=indent,
+                                           subsequent_indent=indent)
+
+    def _get_help_string(self, action):
+        return action.help
+
+
+class RawDescriptionHelpFormatter(HelpFormatter):
+    """Help message formatter which retains any formatting in descriptions.
+
+    Only the name of this class is considered a public API. All the methods
+    provided by the class are considered an implementation detail.
+    """
+
+    def _fill_text(self, text, width, indent):
+        return ''.join([indent + line for line in text.splitlines(True)])
+
+
+class RawTextHelpFormatter(RawDescriptionHelpFormatter):
+    """Help message formatter which retains formatting of all help text.
+
+    Only the name of this class is considered a public API. All the methods
+    provided by the class are considered an implementation detail.
+    """
+
+    def _split_lines(self, text, width):
+        return text.splitlines()
+
+
+class ArgumentDefaultsHelpFormatter(HelpFormatter):
+    """Help message formatter which adds default values to argument help.
+
+    Only the name of this class is considered a public API. All the methods
+    provided by the class are considered an implementation detail.
+    """
+
+    def _get_help_string(self, action):
+        help = action.help
+        if '%(default)' not in action.help:
+            if action.default is not SUPPRESS:
+                defaulting_nargs = [OPTIONAL, ZERO_OR_MORE]
+                if action.option_strings or action.nargs in defaulting_nargs:
+                    help += ' (default: %(default)s)'
+        return help
+
+
+# =====================
+# Options and Arguments
+# =====================
+
+def _get_action_name(argument):
+    if argument is None:
+        return None
+    elif argument.option_strings:
+        return  '/'.join(argument.option_strings)
+    elif argument.metavar not in (None, SUPPRESS):
+        return argument.metavar
+    elif argument.dest not in (None, SUPPRESS):
+        return argument.dest
+    else:
+        return None
+
+
+class ArgumentError(Exception):
+    """An error from creating or using an argument (optional or positional).
+
+    The string value of this exception is the message, augmented with
+    information about the argument that caused it.
+    """
+
+    def __init__(self, argument, message):
+        self.argument_name = _get_action_name(argument)
+        self.message = message
+
+    def __str__(self):
+        if self.argument_name is None:
+            format = '%(message)s'
+        else:
+            format = 'argument %(argument_name)s: %(message)s'
+        return format % dict(message=self.message,
+                             argument_name=self.argument_name)
+
+
+class ArgumentTypeError(Exception):
+    """An error from trying to convert a command line string to a type."""
+    pass
+
+
+# ==============
+# Action classes
+# ==============
+
+class Action(_AttributeHolder):
+    """Information about how to convert command line strings to Python objects.
+
+    Action objects are used by an ArgumentParser to represent the information
+    needed to parse a single argument from one or more strings from the
+    command line. The keyword arguments to the Action constructor are also
+    all attributes of Action instances.
+
+    Keyword Arguments:
+
+        - option_strings -- A list of command-line option strings which
+            should be associated with this action.
+
+        - dest -- The name of the attribute to hold the created object(s)
+
+        - nargs -- The number of command-line arguments that should be
+            consumed. By default, one argument will be consumed and a single
+            value will be produced.  Other values include:
+                - N (an integer) consumes N arguments (and produces a list)
+                - '?' consumes zero or one arguments
+                - '*' consumes zero or more arguments (and produces a list)
+                - '+' consumes one or more arguments (and produces a list)
+            Note that the difference between the default and nargs=1 is that
+            with the default, a single value will be produced, while with
+            nargs=1, a list containing a single value will be produced.
+
+        - const -- The value to be produced if the option is specified and the
+            option uses an action that takes no values.
+
+        - default -- The value to be produced if the option is not specified.
+
+        - type -- The type which the command-line arguments should be converted
+            to, should be one of 'string', 'int', 'float', 'complex' or a
+            callable object that accepts a single string argument. If None,
+            'string' is assumed.
+
+        - choices -- A container of values that should be allowed. If not None,
+            after a command-line argument has been converted to the appropriate
+            type, an exception will be raised if it is not a member of this
+            collection.
+
+        - required -- True if the action must always be specified at the
+            command line. This is only meaningful for optional command-line
+            arguments.
+
+        - help -- The help string describing the argument.
+
+        - metavar -- The name to be used for the option's argument with the
+            help string. If None, the 'dest' value will be used as the name.
+    """
+
+    def __init__(self,
+                 option_strings,
+                 dest,
+                 nargs=None,
+                 const=None,
+                 default=None,
+                 type=None,
+                 choices=None,
+                 required=False,
+                 help=None,
+                 metavar=None):
+        self.option_strings = option_strings
+        self.dest = dest
+        self.nargs = nargs
+        self.const = const
+        self.default = default
+        self.type = type
+        self.choices = choices
+        self.required = required
+        self.help = help
+        self.metavar = metavar
+
+    def _get_kwargs(self):
+        names = [
+            'option_strings',
+            'dest',
+            'nargs',
+            'const',
+            'default',
+            'type',
+            'choices',
+            'help',
+            'metavar',
+        ]
+        return [(name, getattr(self, name)) for name in names]
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        raise NotImplementedError(_('.__call__() not defined'))
+
+
+class _StoreAction(Action):
+
+    def __init__(self,
+                 option_strings,
+                 dest,
+                 nargs=None,
+                 const=None,
+                 default=None,
+                 type=None,
+                 choices=None,
+                 required=False,
+                 help=None,
+                 metavar=None):
+        if nargs == 0:
+            raise ValueError('nargs for store actions must be > 0; if you '
+                             'have nothing to store, actions such as store '
+                             'true or store const may be more appropriate')
+        if const is not None and nargs != OPTIONAL:
+            raise ValueError('nargs must be %r to supply const' % OPTIONAL)
+        super(_StoreAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            nargs=nargs,
+            const=const,
+            default=default,
+            type=type,
+            choices=choices,
+            required=required,
+            help=help,
+            metavar=metavar)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        setattr(namespace, self.dest, values)
+
+
+class _StoreConstAction(Action):
+
+    def __init__(self,
+                 option_strings,
+                 dest,
+                 const,
+                 default=None,
+                 required=False,
+                 help=None,
+                 metavar=None):
+        super(_StoreConstAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            nargs=0,
+            const=const,
+            default=default,
+            required=required,
+            help=help)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        setattr(namespace, self.dest, self.const)
+
+
+class _StoreTrueAction(_StoreConstAction):
+
+    def __init__(self,
+                 option_strings,
+                 dest,
+                 default=False,
+                 required=False,
+                 help=None):
+        super(_StoreTrueAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            const=True,
+            default=default,
+            required=required,
+            help=help)
+
+
+class _StoreFalseAction(_StoreConstAction):
+
+    def __init__(self,
+                 option_strings,
+                 dest,
+                 default=True,
+                 required=False,
+                 help=None):
+        super(_StoreFalseAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            const=False,
+            default=default,
+            required=required,
+            help=help)
+
+
+class _AppendAction(Action):
+
+    def __init__(self,
+                 option_strings,
+                 dest,
+                 nargs=None,
+                 const=None,
+                 default=None,
+                 type=None,
+                 choices=None,
+                 required=False,
+                 help=None,
+                 metavar=None):
+        if nargs == 0:
+            raise ValueError('nargs for append actions must be > 0; if arg '
+                             'strings are not supplying the value to append, '
+                             'the append const action may be more appropriate')
+        if const is not None and nargs != OPTIONAL:
+            raise ValueError('nargs must be %r to supply const' % OPTIONAL)
+        super(_AppendAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            nargs=nargs,
+            const=const,
+            default=default,
+            type=type,
+            choices=choices,
+            required=required,
+            help=help,
+            metavar=metavar)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        items = _copy.copy(_ensure_value(namespace, self.dest, []))
+        items.append(values)
+        setattr(namespace, self.dest, items)
+
+
+class _AppendConstAction(Action):
+
+    def __init__(self,
+                 option_strings,
+                 dest,
+                 const,
+                 default=None,
+                 required=False,
+                 help=None,
+                 metavar=None):
+        super(_AppendConstAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            nargs=0,
+            const=const,
+            default=default,
+            required=required,
+            help=help,
+            metavar=metavar)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        items = _copy.copy(_ensure_value(namespace, self.dest, []))
+        items.append(self.const)
+        setattr(namespace, self.dest, items)
+
+
+class _CountAction(Action):
+
+    def __init__(self,
+                 option_strings,
+                 dest,
+                 default=None,
+                 required=False,
+                 help=None):
+        super(_CountAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            nargs=0,
+            default=default,
+            required=required,
+            help=help)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        new_count = _ensure_value(namespace, self.dest, 0) + 1
+        setattr(namespace, self.dest, new_count)
+
+
+class _HelpAction(Action):
+
+    def __init__(self,
+                 option_strings,
+                 dest=SUPPRESS,
+                 default=SUPPRESS,
+                 help=None):
+        super(_HelpAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            default=default,
+            nargs=0,
+            help=help)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        parser.print_help()
+        parser.exit()
+
+
+class _VersionAction(Action):
+
+    def __init__(self,
+                 option_strings,
+                 version=None,
+                 dest=SUPPRESS,
+                 default=SUPPRESS,
+                 help="show program's version number and exit"):
+        super(_VersionAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            default=default,
+            nargs=0,
+            help=help)
+        self.version = version
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        version = self.version
+        if version is None:
+            version = parser.version
+        formatter = parser._get_formatter()
+        formatter.add_text(version)
+        parser.exit(message=formatter.format_help())
+
+
+class _SubParsersAction(Action):
+
+    class _ChoicesPseudoAction(Action):
+
+        def __init__(self, name, help):
+            sup = super(_SubParsersAction._ChoicesPseudoAction, self)
+            sup.__init__(option_strings=[], dest=name, help=help)
+
+    def __init__(self,
+                 option_strings,
+                 prog,
+                 parser_class,
+                 dest=SUPPRESS,
+                 help=None,
+                 metavar=None):
+
+        self._prog_prefix = prog
+        self._parser_class = parser_class
+        self._name_parser_map = {}
+        self._choices_actions = []
+
+        super(_SubParsersAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            nargs=PARSER,
+            choices=self._name_parser_map,
+            help=help,
+            metavar=metavar)
+
+    def add_parser(self, name, **kwargs):
+        # set prog from the existing prefix
+        if kwargs.get('prog') is None:
+            kwargs['prog'] = '%s %s' % (self._prog_prefix, name)
+
+        # create a pseudo-action to hold the choice help
+        if 'help' in kwargs:
+            help = kwargs.pop('help')
+            choice_action = self._ChoicesPseudoAction(name, help)
+            self._choices_actions.append(choice_action)
+
+        # create the parser and add it to the map
+        parser = self._parser_class(**kwargs)
+        self._name_parser_map[name] = parser
+        return parser
+
+    def _get_subactions(self):
+        return self._choices_actions
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        parser_name = values[0]
+        arg_strings = values[1:]
+
+        # set the parser name if requested
+        if self.dest is not SUPPRESS:
+            setattr(namespace, self.dest, parser_name)
+
+        # select the parser
+        try:
+            parser = self._name_parser_map[parser_name]
+        except KeyError:
+            tup = parser_name, ', '.join(self._name_parser_map)
+            msg = _('unknown parser %r (choices: %s)' % tup)
+            raise ArgumentError(self, msg)
+
+        # parse all the remaining options into the namespace
+        # store any unrecognized options on the object, so that the top
+        # level parser can decide what to do with them
+        namespace, arg_strings = parser.parse_known_args(arg_strings, namespace)
+        if arg_strings:
+            vars(namespace).setdefault(_UNRECOGNIZED_ARGS_ATTR, [])
+            getattr(namespace, _UNRECOGNIZED_ARGS_ATTR).extend(arg_strings)
+
+
+# ==============
+# Type classes
+# ==============
+
+class FileType(object):
+    """Factory for creating file object types
+
+    Instances of FileType are typically passed as type= arguments to the
+    ArgumentParser add_argument() method.
+
+    Keyword Arguments:
+        - mode -- A string indicating how the file is to be opened. Accepts the
+            same values as the builtin open() function.
+        - bufsize -- The file's desired buffer size. Accepts the same values as
+            the builtin open() function.
+    """
+
+    def __init__(self, mode='r', bufsize=None):
+        self._mode = mode
+        self._bufsize = bufsize
+
+    def __call__(self, string):
+        # the special argument "-" means sys.std{in,out}
+        if string == '-':
+            if 'r' in self._mode:
+                return _sys.stdin
+            elif 'w' in self._mode:
+                return _sys.stdout
+            else:
+                msg = _('argument "-" with mode %r' % self._mode)
+                raise ValueError(msg)
+
+        # all other arguments are used as file names
+        if self._bufsize:
+            return open(string, self._mode, self._bufsize)
+        else:
+            return open(string, self._mode)
+
+    def __repr__(self):
+        args = [self._mode, self._bufsize]
+        args_str = ', '.join([repr(arg) for arg in args if arg is not None])
+        return '%s(%s)' % (type(self).__name__, args_str)
+
+# ===========================
+# Optional and Positional Parsing
+# ===========================
+
+class Namespace(_AttributeHolder):
+    """Simple object for storing attributes.
+
+    Implements equality by attribute names and values, and provides a simple
+    string representation.
+    """
+
+    def __init__(self, **kwargs):
+        for name in kwargs:
+            setattr(self, name, kwargs[name])
+
+    __hash__ = None
+
+    def __eq__(self, other):
+        return vars(self) == vars(other)
+
+    def __ne__(self, other):
+        return not (self == other)
+
+    def __contains__(self, key):
+        return key in self.__dict__
+
+
+class _ActionsContainer(object):
+
+    def __init__(self,
+                 description,
+                 prefix_chars,
+                 argument_default,
+                 conflict_handler):
+        super(_ActionsContainer, self).__init__()
+
+        self.description = description
+        self.argument_default = argument_default
+        self.prefix_chars = prefix_chars
+        self.conflict_handler = conflict_handler
+
+        # set up registries
+        self._registries = {}
+
+        # register actions
+        self.register('action', None, _StoreAction)
+        self.register('action', 'store', _StoreAction)
+        self.register('action', 'store_const', _StoreConstAction)
+        self.register('action', 'store_true', _StoreTrueAction)
+        self.register('action', 'store_false', _StoreFalseAction)
+        self.register('action', 'append', _AppendAction)
+        self.register('action', 'append_const', _AppendConstAction)
+        self.register('action', 'count', _CountAction)
+        self.register('action', 'help', _HelpAction)
+        self.register('action', 'version', _VersionAction)
+        self.register('action', 'parsers', _SubParsersAction)
+
+        # raise an exception if the conflict handler is invalid
+        self._get_handler()
+
+        # action storage
+        self._actions = []
+        self._option_string_actions = {}
+
+        # groups
+        self._action_groups = []
+        self._mutually_exclusive_groups = []
+
+        # defaults storage
+        self._defaults = {}
+
+        # determines whether an "option" looks like a negative number
+        self._negative_number_matcher = _re.compile(r'^-\d+$|^-\d*\.\d+$')
+
+        # whether or not there are any optionals that look like negative
+        # numbers -- uses a list so it can be shared and edited
+        self._has_negative_number_optionals = []
+
+    # ====================
+    # Registration methods
+    # ====================
+    def register(self, registry_name, value, object):
+        registry = self._registries.setdefault(registry_name, {})
+        registry[value] = object
+
+    def _registry_get(self, registry_name, value, default=None):
+        return self._registries[registry_name].get(value, default)
+
+    # ==================================
+    # Namespace default accessor methods
+    # ==================================
+    def set_defaults(self, **kwargs):
+        self._defaults.update(kwargs)
+
+        # if these defaults match any existing arguments, replace
+        # the previous default on the object with the new one
+        for action in self._actions:
+            if action.dest in kwargs:
+                action.default = kwargs[action.dest]
+
+    def get_default(self, dest):
+        for action in self._actions:
+            if action.dest == dest and action.default is not None:
+                return action.default
+        return self._defaults.get(dest, None)
+
+
+    # =======================
+    # Adding argument actions
+    # =======================
+    def add_argument(self, *args, **kwargs):
+        """
+        add_argument(dest, ..., name=value, ...)
+        add_argument(option_string, option_string, ..., name=value, ...)
+        """
+
+        # if no positional args are supplied or only one is supplied and
+        # it doesn't look like an option string, parse a positional
+        # argument
+        chars = self.prefix_chars
+        if not args or len(args) == 1 and args[0][0] not in chars:
+            if args and 'dest' in kwargs:
+                raise ValueError('dest supplied twice for positional argument')
+            kwargs = self._get_positional_kwargs(*args, **kwargs)
+
+        # otherwise, we're adding an optional argument
+        else:
+            kwargs = self._get_optional_kwargs(*args, **kwargs)
+
+        # if no default was supplied, use the parser-level default
+        if 'default' not in kwargs:
+            dest = kwargs['dest']
+            if dest in self._defaults:
+                kwargs['default'] = self._defaults[dest]
+            elif self.argument_default is not None:
+                kwargs['default'] = self.argument_default
+
+        # create the action object, and add it to the parser
+        action_class = self._pop_action_class(kwargs)
+        if not _callable(action_class):
+            raise ValueError('unknown action "%s"' % action_class)
+        action = action_class(**kwargs)
+
+        # raise an error if the action type is not callable
+        type_func = self._registry_get('type', action.type, action.type)
+        if not _callable(type_func):
+            raise ValueError('%r is not callable' % type_func)
+
+        return self._add_action(action)
+
+    def add_argument_group(self, *args, **kwargs):
+        group = _ArgumentGroup(self, *args, **kwargs)
+        self._action_groups.append(group)
+        return group
+
+    def add_mutually_exclusive_group(self, **kwargs):
+        group = _MutuallyExclusiveGroup(self, **kwargs)
+        self._mutually_exclusive_groups.append(group)
+        return group
+
+    def _add_action(self, action):
+        # resolve any conflicts
+        self._check_conflict(action)
+
+        # add to actions list
+        self._actions.append(action)
+        action.container = self
+
+        # index the action by any option strings it has
+        for option_string in action.option_strings:
+            self._option_string_actions[option_string] = action
+
+        # set the flag if any option strings look like negative numbers
+        for option_string in action.option_strings:
+            if self._negative_number_matcher.match(option_string):
+                if not self._has_negative_number_optionals:
+                    self._has_negative_number_optionals.append(True)
+
+        # return the created action
+        return action
+
+    def _remove_action(self, action):
+        self._actions.remove(action)
+
+    def _add_container_actions(self, container):
+        # collect groups by titles
+        title_group_map = {}
+        for group in self._action_groups:
+            if group.title in title_group_map:
+                msg = _('cannot merge actions - two groups are named %r')
+                raise ValueError(msg % (group.title))
+            title_group_map[group.title] = group
+
+        # map each action to its group
+        group_map = {}
+        for group in container._action_groups:
+
+            # if a group with the title exists, use that, otherwise
+            # create a new group matching the container's group
+            if group.title not in title_group_map:
+                title_group_map[group.title] = self.add_argument_group(
+                    title=group.title,
+                    description=group.description,
+                    conflict_handler=group.conflict_handler)
+
+            # map the actions to their new group
+            for action in group._group_actions:
+                group_map[action] = title_group_map[group.title]
+
+        # add container's mutually exclusive groups
+        # NOTE: if add_mutually_exclusive_group ever gains title= and
+        # description= then this code will need to be expanded as above
+        for group in container._mutually_exclusive_groups:
+            mutex_group = self.add_mutually_exclusive_group(
+                required=group.required)
+
+            # map the actions to their new mutex group
+            for action in group._group_actions:
+                group_map[action] = mutex_group
+
+        # add all actions to this container or their group
+        for action in container._actions:
+            group_map.get(action, self)._add_action(action)
+
+    def _get_positional_kwargs(self, dest, **kwargs):
+        # make sure required is not specified
+        if 'required' in kwargs:
+            msg = _("'required' is an invalid argument for positionals")
+            raise TypeError(msg)
+
+        # mark positional arguments as required if at least one is
+        # always required
+        if kwargs.get('nargs') not in [OPTIONAL, ZERO_OR_MORE]:
+            kwargs['required'] = True
+        if kwargs.get('nargs') == ZERO_OR_MORE and 'default' not in kwargs:
+            kwargs['required'] = True
+
+        # return the keyword arguments with no option strings
+        return dict(kwargs, dest=dest, option_strings=[])
+
+    def _get_optional_kwargs(self, *args, **kwargs):
+        # determine short and long option strings
+        option_strings = []
+        long_option_strings = []
+        for option_string in args:
+            # error on strings that don't start with an appropriate prefix
+            if not option_string[0] in self.prefix_chars:
+                msg = _('invalid option string %r: '
+                        'must start with a character %r')
+                tup = option_string, self.prefix_chars
+                raise ValueError(msg % tup)
+
+            # strings starting with two prefix characters are long options
+            option_strings.append(option_string)
+            if option_string[0] in self.prefix_chars:
+                if len(option_string) > 1:
+                    if option_string[1] in self.prefix_chars:
+                        long_option_strings.append(option_string)
+
+        # infer destination, '--foo-bar' -> 'foo_bar' and '-x' -> 'x'
+        dest = kwargs.pop('dest', None)
+        if dest is None:
+            if long_option_strings:
+                dest_option_string = long_option_strings[0]
+            else:
+                dest_option_string = option_strings[0]
+            dest = dest_option_string.lstrip(self.prefix_chars)
+            if not dest:
+                msg = _('dest= is required for options like %r')
+                raise ValueError(msg % option_string)
+            dest = dest.replace('-', '_')
+
+        # return the updated keyword arguments
+        return dict(kwargs, dest=dest, option_strings=option_strings)
+
+    def _pop_action_class(self, kwargs, default=None):
+        action = kwargs.pop('action', default)
+        return self._registry_get('action', action, action)
+
+    def _get_handler(self):
+        # determine function from conflict handler string
+        handler_func_name = '_handle_conflict_%s' % self.conflict_handler
+        try:
+            return getattr(self, handler_func_name)
+        except AttributeError:
+            msg = _('invalid conflict_resolution value: %r')
+            raise ValueError(msg % self.conflict_handler)
+
+    def _check_conflict(self, action):
+
+        # find all options that conflict with this option
+        confl_optionals = []
+        for option_string in action.option_strings:
+            if option_string in self._option_string_actions:
+                confl_optional = self._option_string_actions[option_string]
+                confl_optionals.append((option_string, confl_optional))
+
+        # resolve any conflicts
+        if confl_optionals:
+            conflict_handler = self._get_handler()
+            conflict_handler(action, confl_optionals)
+
+    def _handle_conflict_error(self, action, conflicting_actions):
+        message = _('conflicting option string(s): %s')
+        conflict_string = ', '.join([option_string
+                                     for option_string, action
+                                     in conflicting_actions])
+        raise ArgumentError(action, message % conflict_string)
+
+    def _handle_conflict_resolve(self, action, conflicting_actions):
+
+        # remove all conflicting options
+        for option_string, action in conflicting_actions:
+
+            # remove the conflicting option
+            action.option_strings.remove(option_string)
+            self._option_string_actions.pop(option_string, None)
+
+            # if the option now has no option string, remove it from the
+            # container holding it
+            if not action.option_strings:
+                action.container._remove_action(action)
+
+
+class _ArgumentGroup(_ActionsContainer):
+
+    def __init__(self, container, title=None, description=None, **kwargs):
+        # add any missing keyword arguments by checking the container
+        update = kwargs.setdefault
+        update('conflict_handler', container.conflict_handler)
+        update('prefix_chars', container.prefix_chars)
+        update('argument_default', container.argument_default)
+        super_init = super(_ArgumentGroup, self).__init__
+        super_init(description=description, **kwargs)
+
+        # group attributes
+        self.title = title
+        self._group_actions = []
+
+        # share most attributes with the container
+        self._registries = container._registries
+        self._actions = container._actions
+        self._option_string_actions = container._option_string_actions
+        self._defaults = container._defaults
+        self._has_negative_number_optionals = \
+            container._has_negative_number_optionals
+
+    def _add_action(self, action):
+        action = super(_ArgumentGroup, self)._add_action(action)
+        self._group_actions.append(action)
+        return action
+
+    def _remove_action(self, action):
+        super(_ArgumentGroup, self)._remove_action(action)
+        self._group_actions.remove(action)
+
+
+class _MutuallyExclusiveGroup(_ArgumentGroup):
+
+    def __init__(self, container, required=False):
+        super(_MutuallyExclusiveGroup, self).__init__(container)
+        self.required = required
+        self._container = container
+
+    def _add_action(self, action):
+        if action.required:
+            msg = _('mutually exclusive arguments must be optional')
+            raise ValueError(msg)
+        action = self._container._add_action(action)
+        self._group_actions.append(action)
+        return action
+
+    def _remove_action(self, action):
+        self._container._remove_action(action)
+        self._group_actions.remove(action)
+
+
+class ArgumentParser(_AttributeHolder, _ActionsContainer):
+    """Object for parsing command line strings into Python objects.
+
+    Keyword Arguments:
+        - prog -- The name of the program (default: sys.argv[0])
+        - usage -- A usage message (default: auto-generated from arguments)
+        - description -- A description of what the program does
+        - epilog -- Text following the argument descriptions
+        - parents -- Parsers whose arguments should be copied into this one
+        - formatter_class -- HelpFormatter class for printing help messages
+        - prefix_chars -- Characters that prefix optional arguments
+        - fromfile_prefix_chars -- Characters that prefix files containing
+            additional arguments
+        - argument_default -- The default value for all arguments
+        - conflict_handler -- String indicating how to handle conflicts
+        - add_help -- Add a -h/-help option
+    """
+
+    def __init__(self,
+                 prog=None,
+                 usage=None,
+                 description=None,
+                 epilog=None,
+                 version=None,
+                 parents=[],
+                 formatter_class=HelpFormatter,
+                 prefix_chars='-',
+                 fromfile_prefix_chars=None,
+                 argument_default=None,
+                 conflict_handler='error',
+                 add_help=True):
+
+        if version is not None:
+            import warnings
+            warnings.warn(
+                """The "version" argument to ArgumentParser is deprecated. """
+                """Please use """
+                """"add_argument(..., action='version', version="N", ...)" """
+                """instead""", DeprecationWarning)
+
+        superinit = super(ArgumentParser, self).__init__
+        superinit(description=description,
+                  prefix_chars=prefix_chars,
+                  argument_default=argument_default,
+                  conflict_handler=conflict_handler)
+
+        # default setting for prog
+        if prog is None:
+            prog = _os.path.basename(_sys.argv[0])
+
+        self.prog = prog
+        self.usage = usage
+        self.epilog = epilog
+        self.version = version
+        self.formatter_class = formatter_class
+        self.fromfile_prefix_chars = fromfile_prefix_chars
+        self.add_help = add_help
+
+        add_group = self.add_argument_group
+        self._positionals = add_group(_('positional arguments'))
+        self._optionals = add_group(_('optional arguments'))
+        self._subparsers = None
+
+        # register types
+        def identity(string):
+            return string
+        self.register('type', None, identity)
+
+        # add help and version arguments if necessary
+        # (using explicit default to override global argument_default)
+        if '-' in prefix_chars:
+            default_prefix = '-'
+        else:
+            default_prefix = prefix_chars[0]
+        if self.add_help:
+            self.add_argument(
+                default_prefix+'h', default_prefix*2+'help',
+                action='help', default=SUPPRESS,
+                help=_('show this help message and exit'))
+        if self.version:
+            self.add_argument(
+                default_prefix+'v', default_prefix*2+'version',
+                action='version', default=SUPPRESS,
+                version=self.version,
+                help=_("show program's version number and exit"))
+
+        # add parent arguments and defaults
+        for parent in parents:
+            self._add_container_actions(parent)
+            try:
+                defaults = parent._defaults
+            except AttributeError:
+                pass
+            else:
+                self._defaults.update(defaults)
+
+    # =======================
+    # Pretty __repr__ methods
+    # =======================
+    def _get_kwargs(self):
+        names = [
+            'prog',
+            'usage',
+            'description',
+            'version',
+            'formatter_class',
+            'conflict_handler',
+            'add_help',
+        ]
+        return [(name, getattr(self, name)) for name in names]
+
+    # ==================================
+    # Optional/Positional adding methods
+    # ==================================
+    def add_subparsers(self, **kwargs):
+        if self._subparsers is not None:
+            self.error(_('cannot have multiple subparser arguments'))
+
+        # add the parser class to the arguments if it's not present
+        kwargs.setdefault('parser_class', type(self))
+
+        if 'title' in kwargs or 'description' in kwargs:
+            title = _(kwargs.pop('title', 'subcommands'))
+            description = _(kwargs.pop('description', None))
+            self._subparsers = self.add_argument_group(title, description)
+        else:
+            self._subparsers = self._positionals
+
+        # prog defaults to the usage message of this parser, skipping
+        # optional arguments and with no "usage:" prefix
+        if kwargs.get('prog') is None:
+            formatter = self._get_formatter()
+            positionals = self._get_positional_actions()
+            groups = self._mutually_exclusive_groups
+            formatter.add_usage(self.usage, positionals, groups, '')
+            kwargs['prog'] = formatter.format_help().strip()
+
+        # create the parsers action and add it to the positionals list
+        parsers_class = self._pop_action_class(kwargs, 'parsers')
+        action = parsers_class(option_strings=[], **kwargs)
+        self._subparsers._add_action(action)
+
+        # return the created parsers action
+        return action
+
+    def _add_action(self, action):
+        if action.option_strings:
+            self._optionals._add_action(action)
+        else:
+            self._positionals._add_action(action)
+        return action
+
+    def _get_optional_actions(self):
+        return [action
+                for action in self._actions
+                if action.option_strings]
+
+    def _get_positional_actions(self):
+        return [action
+                for action in self._actions
+                if not action.option_strings]
+
+    # =====================================
+    # Command line argument parsing methods
+    # =====================================
+    def parse_args(self, args=None, namespace=None):
+        args, argv = self.parse_known_args(args, namespace)
+        if argv:
+            msg = _('unrecognized arguments: %s')
+            self.error(msg % ' '.join(argv))
+        return args
+
+    def parse_known_args(self, args=None, namespace=None):
+        # args default to the system args
+        if args is None:
+            args = _sys.argv[1:]
+
+        # default Namespace built from parser defaults
+        if namespace is None:
+            namespace = Namespace()
+
+        # add any action defaults that aren't present
+        for action in self._actions:
+            if action.dest is not SUPPRESS:
+                if not hasattr(namespace, action.dest):
+                    if action.default is not SUPPRESS:
+                        default = action.default
+                        if isinstance(action.default, basestring):
+                            default = self._get_value(action, default)
+                        setattr(namespace, action.dest, default)
+
+        # add any parser defaults that aren't present
+        for dest in self._defaults:
+            if not hasattr(namespace, dest):
+                setattr(namespace, dest, self._defaults[dest])
+
+        # parse the arguments and exit if there are any errors
+        try:
+            namespace, args = self._parse_known_args(args, namespace)
+            if hasattr(namespace, _UNRECOGNIZED_ARGS_ATTR):
+                args.extend(getattr(namespace, _UNRECOGNIZED_ARGS_ATTR))
+                delattr(namespace, _UNRECOGNIZED_ARGS_ATTR)
+            return namespace, args
+        except ArgumentError:
+            err = _sys.exc_info()[1]
+            self.error(str(err))
+
+    def _parse_known_args(self, arg_strings, namespace):
+        # replace arg strings that are file references
+        if self.fromfile_prefix_chars is not None:
+            arg_strings = self._read_args_from_files(arg_strings)
+
+        # map all mutually exclusive arguments to the other arguments
+        # they can't occur with
+        action_conflicts = {}
+        for mutex_group in self._mutually_exclusive_groups:
+            group_actions = mutex_group._group_actions
+            for i, mutex_action in enumerate(mutex_group._group_actions):
+                conflicts = action_conflicts.setdefault(mutex_action, [])
+                conflicts.extend(group_actions[:i])
+                conflicts.extend(group_actions[i + 1:])
+
+        # find all option indices, and determine the arg_string_pattern
+        # which has an 'O' if there is an option at an index,
+        # an 'A' if there is an argument, or a '-' if there is a '--'
+        option_string_indices = {}
+        arg_string_pattern_parts = []
+        arg_strings_iter = iter(arg_strings)
+        for i, arg_string in enumerate(arg_strings_iter):
+
+            # all args after -- are non-options
+            if arg_string == '--':
+                arg_string_pattern_parts.append('-')
+                for arg_string in arg_strings_iter:
+                    arg_string_pattern_parts.append('A')
+
+            # otherwise, add the arg to the arg strings
+            # and note the index if it was an option
+            else:
+                option_tuple = self._parse_optional(arg_string)
+                if option_tuple is None:
+                    pattern = 'A'
+                else:
+                    option_string_indices[i] = option_tuple
+                    pattern = 'O'
+                arg_string_pattern_parts.append(pattern)
+
+        # join the pieces together to form the pattern
+        arg_strings_pattern = ''.join(arg_string_pattern_parts)
+
+        # converts arg strings to the appropriate and then takes the action
+        seen_actions = set()
+        seen_non_default_actions = set()
+
+        def take_action(action, argument_strings, option_string=None):
+            seen_actions.add(action)
+            argument_values = self._get_values(action, argument_strings)
+
+            # error if this argument is not allowed with other previously
+            # seen arguments, assuming that actions that use the default
+            # value don't really count as "present"
+            if argument_values is not action.default:
+                seen_non_default_actions.add(action)
+                for conflict_action in action_conflicts.get(action, []):
+                    if conflict_action in seen_non_default_actions:
+                        msg = _('not allowed with argument %s')
+                        action_name = _get_action_name(conflict_action)
+                        raise ArgumentError(action, msg % action_name)
+
+            # take the action if we didn't receive a SUPPRESS value
+            # (e.g. from a default)
+            if argument_values is not SUPPRESS:
+                action(self, namespace, argument_values, option_string)
+
+        # function to convert arg_strings into an optional action
+        def consume_optional(start_index):
+
+            # get the optional identified at this index
+            option_tuple = option_string_indices[start_index]
+            action, option_string, explicit_arg = option_tuple
+
+            # identify additional optionals in the same arg string
+            # (e.g. -xyz is the same as -x -y -z if no args are required)
+            match_argument = self._match_argument
+            action_tuples = []
+            while True:
+
+                # if we found no optional action, skip it
+                if action is None:
+                    extras.append(arg_strings[start_index])
+                    return start_index + 1
+
+                # if there is an explicit argument, try to match the
+                # optional's string arguments to only this
+                if explicit_arg is not None:
+                    arg_count = match_argument(action, 'A')
+
+                    # if the action is a single-dash option and takes no
+                    # arguments, try to parse more single-dash options out
+                    # of the tail of the option string
+                    chars = self.prefix_chars
+                    if arg_count == 0 and option_string[1] not in chars:
+                        action_tuples.append((action, [], option_string))
+                        char = option_string[0]
+                        option_string = char + explicit_arg[0]
+                        new_explicit_arg = explicit_arg[1:] or None
+                        optionals_map = self._option_string_actions
+                        if option_string in optionals_map:
+                            action = optionals_map[option_string]
+                            explicit_arg = new_explicit_arg
+                        else:
+                            msg = _('ignored explicit argument %r')
+                            raise ArgumentError(action, msg % explicit_arg)
+
+                    # if the action expect exactly one argument, we've
+                    # successfully matched the option; exit the loop
+                    elif arg_count == 1:
+                        stop = start_index + 1
+                        args = [explicit_arg]
+                        action_tuples.append((action, args, option_string))
+                        break
+
+                    # error if a double-dash option did not use the
+                    # explicit argument
+                    else:
+                        msg = _('ignored explicit argument %r')
+                        raise ArgumentError(action, msg % explicit_arg)
+
+                # if there is no explicit argument, try to match the
+                # optional's string arguments with the following strings
+                # if successful, exit the loop
+                else:
+                    start = start_index + 1
+                    selected_patterns = arg_strings_pattern[start:]
+                    arg_count = match_argument(action, selected_patterns)
+                    stop = start + arg_count
+                    args = arg_strings[start:stop]
+                    action_tuples.append((action, args, option_string))
+                    break
+
+            # add the Optional to the list and return the index at which
+            # the Optional's string args stopped
+            assert action_tuples
+            for action, args, option_string in action_tuples:
+                take_action(action, args, option_string)
+            return stop
+
+        # the list of Positionals left to be parsed; this is modified
+        # by consume_positionals()
+        positionals = self._get_positional_actions()
+
+        # function to convert arg_strings into positional actions
+        def consume_positionals(start_index):
+            # match as many Positionals as possible
+            match_partial = self._match_arguments_partial
+            selected_pattern = arg_strings_pattern[start_index:]
+            arg_counts = match_partial(positionals, selected_pattern)
+
+            # slice off the appropriate arg strings for each Positional
+            # and add the Positional and its args to the list
+            for action, arg_count in zip(positionals, arg_counts):
+                args = arg_strings[start_index: start_index + arg_count]
+                start_index += arg_count
+                take_action(action, args)
+
+            # slice off the Positionals that we just parsed and return the
+            # index at which the Positionals' string args stopped
+            positionals[:] = positionals[len(arg_counts):]
+            return start_index
+
+        # consume Positionals and Optionals alternately, until we have
+        # passed the last option string
+        extras = []
+        start_index = 0
+        if option_string_indices:
+            max_option_string_index = max(option_string_indices)
+        else:
+            max_option_string_index = -1
+        while start_index <= max_option_string_index:
+
+            # consume any Positionals preceding the next option
+            next_option_string_index = min([
+                index
+                for index in option_string_indices
+                if index >= start_index])
+            if start_index != next_option_string_index:
+                positionals_end_index = consume_positionals(start_index)
+
+                # only try to parse the next optional if we didn't consume
+                # the option string during the positionals parsing
+                if positionals_end_index > start_index:
+                    start_index = positionals_end_index
+                    continue
+                else:
+                    start_index = positionals_end_index
+
+            # if we consumed all the positionals we could and we're not
+            # at the index of an option string, there were extra arguments
+            if start_index not in option_string_indices:
+                strings = arg_strings[start_index:next_option_string_index]
+                extras.extend(strings)
+                start_index = next_option_string_index
+
+            # consume the next optional and any arguments for it
+            start_index = consume_optional(start_index)
+
+        # consume any positionals following the last Optional
+        stop_index = consume_positionals(start_index)
+
+        # if we didn't consume all the argument strings, there were extras
+        extras.extend(arg_strings[stop_index:])
+
+        # if we didn't use all the Positional objects, there were too few
+        # arg strings supplied.
+        if positionals:
+            self.error(_('too few arguments'))
+
+        # make sure all required actions were present
+        for action in self._actions:
+            if action.required:
+                if action not in seen_actions:
+                    name = _get_action_name(action)
+                    self.error(_('argument %s is required') % name)
+
+        # make sure all required groups had one option present
+        for group in self._mutually_exclusive_groups:
+            if group.required:
+                for action in group._group_actions:
+                    if action in seen_non_default_actions:
+                        break
+
+                # if no actions were used, report the error
+                else:
+                    names = [_get_action_name(action)
+                             for action in group._group_actions
+                             if action.help is not SUPPRESS]
+                    msg = _('one of the arguments %s is required')
+                    self.error(msg % ' '.join(names))
+
+        # return the updated namespace and the extra arguments
+        return namespace, extras
+
+    def _read_args_from_files(self, arg_strings):
+        # expand arguments referencing files
+        new_arg_strings = []
+        for arg_string in arg_strings:
+
+            # for regular arguments, just add them back into the list
+            if arg_string[0] not in self.fromfile_prefix_chars:
+                new_arg_strings.append(arg_string)
+
+            # replace arguments referencing files with the file content
+            else:
+                try:
+                    args_file = open(arg_string[1:])
+                    try:
+                        arg_strings = []
+                        for arg_line in args_file.read().splitlines():
+                            for arg in self.convert_arg_line_to_args(arg_line):
+                                arg_strings.append(arg)
+                        arg_strings = self._read_args_from_files(arg_strings)
+                        new_arg_strings.extend(arg_strings)
+                    finally:
+                        args_file.close()
+                except IOError:
+                    err = _sys.exc_info()[1]
+                    self.error(str(err))
+
+        # return the modified argument list
+        return new_arg_strings
+
+    def convert_arg_line_to_args(self, arg_line):
+        return [arg_line]
+
+    def _match_argument(self, action, arg_strings_pattern):
+        # match the pattern for this action to the arg strings
+        nargs_pattern = self._get_nargs_pattern(action)
+        match = _re.match(nargs_pattern, arg_strings_pattern)
+
+        # raise an exception if we weren't able to find a match
+        if match is None:
+            nargs_errors = {
+                None: _('expected one argument'),
+                OPTIONAL: _('expected at most one argument'),
+                ONE_OR_MORE: _('expected at least one argument'),
+            }
+            default = _('expected %s argument(s)') % action.nargs
+            msg = nargs_errors.get(action.nargs, default)
+            raise ArgumentError(action, msg)
+
+        # return the number of arguments matched
+        return len(match.group(1))
+
+    def _match_arguments_partial(self, actions, arg_strings_pattern):
+        # progressively shorten the actions list by slicing off the
+        # final actions until we find a match
+        result = []
+        for i in range(len(actions), 0, -1):
+            actions_slice = actions[:i]
+            pattern = ''.join([self._get_nargs_pattern(action)
+                               for action in actions_slice])
+            match = _re.match(pattern, arg_strings_pattern)
+            if match is not None:
+                result.extend([len(string) for string in match.groups()])
+                break
+
+        # return the list of arg string counts
+        return result
+
+    def _parse_optional(self, arg_string):
+        # if it's an empty string, it was meant to be a positional
+        if not arg_string:
+            return None
+
+        # if it doesn't start with a prefix, it was meant to be positional
+        if not arg_string[0] in self.prefix_chars:
+            return None
+
+        # if the option string is present in the parser, return the action
+        if arg_string in self._option_string_actions:
+            action = self._option_string_actions[arg_string]
+            return action, arg_string, None
+
+        # if it's just a single character, it was meant to be positional
+        if len(arg_string) == 1:
+            return None
+
+        # if the option string before the "=" is present, return the action
+        if '=' in arg_string:
+            option_string, explicit_arg = arg_string.split('=', 1)
+            if option_string in self._option_string_actions:
+                action = self._option_string_actions[option_string]
+                return action, option_string, explicit_arg
+
+        # search through all possible prefixes of the option string
+        # and all actions in the parser for possible interpretations
+        option_tuples = self._get_option_tuples(arg_string)
+
+        # if multiple actions match, the option string was ambiguous
+        if len(option_tuples) > 1:
+            options = ', '.join([option_string
+                for action, option_string, explicit_arg in option_tuples])
+            tup = arg_string, options
+            self.error(_('ambiguous option: %s could match %s') % tup)
+
+        # if exactly one action matched, this segmentation is good,
+        # so return the parsed action
+        elif len(option_tuples) == 1:
+            option_tuple, = option_tuples
+            return option_tuple
+
+        # if it was not found as an option, but it looks like a negative
+        # number, it was meant to be positional
+        # unless there are negative-number-like options
+        if self._negative_number_matcher.match(arg_string):
+            if not self._has_negative_number_optionals:
+                return None
+
+        # if it contains a space, it was meant to be a positional
+        if ' ' in arg_string:
+            return None
+
+        # it was meant to be an optional but there is no such option
+        # in this parser (though it might be a valid option in a subparser)
+        return None, arg_string, None
+
+    def _get_option_tuples(self, option_string):
+        result = []
+
+        # option strings starting with two prefix characters are only
+        # split at the '='
+        chars = self.prefix_chars
+        if option_string[0] in chars and option_string[1] in chars:
+            if '=' in option_string:
+                option_prefix, explicit_arg = option_string.split('=', 1)
+            else:
+                option_prefix = option_string
+                explicit_arg = None
+            for option_string in self._option_string_actions:
+                if option_string.startswith(option_prefix):
+                    action = self._option_string_actions[option_string]
+                    tup = action, option_string, explicit_arg
+                    result.append(tup)
+
+        # single character options can be concatenated with their arguments
+        # but multiple character options always have to have their argument
+        # separate
+        elif option_string[0] in chars and option_string[1] not in chars:
+            option_prefix = option_string
+            explicit_arg = None
+            short_option_prefix = option_string[:2]
+            short_explicit_arg = option_string[2:]
+
+            for option_string in self._option_string_actions:
+                if option_string == short_option_prefix:
+                    action = self._option_string_actions[option_string]
+                    tup = action, option_string, short_explicit_arg
+                    result.append(tup)
+                elif option_string.startswith(option_prefix):
+                    action = self._option_string_actions[option_string]
+                    tup = action, option_string, explicit_arg
+                    result.append(tup)
+
+        # shouldn't ever get here
+        else:
+            self.error(_('unexpected option string: %s') % option_string)
+
+        # return the collected option tuples
+        return result
+
+    def _get_nargs_pattern(self, action):
+        # in all examples below, we have to allow for '--' args
+        # which are represented as '-' in the pattern
+        nargs = action.nargs
+
+        # the default (None) is assumed to be a single argument
+        if nargs is None:
+            nargs_pattern = '(-*A-*)'
+
+        # allow zero or one arguments
+        elif nargs == OPTIONAL:
+            nargs_pattern = '(-*A?-*)'
+
+        # allow zero or more arguments
+        elif nargs == ZERO_OR_MORE:
+            nargs_pattern = '(-*[A-]*)'
+
+        # allow one or more arguments
+        elif nargs == ONE_OR_MORE:
+            nargs_pattern = '(-*A[A-]*)'
+
+        # allow any number of options or arguments
+        elif nargs == REMAINDER:
+            nargs_pattern = '([-AO]*)'
+
+        # allow one argument followed by any number of options or arguments
+        elif nargs == PARSER:
+            nargs_pattern = '(-*A[-AO]*)'
+
+        # all others should be integers
+        else:
+            nargs_pattern = '(-*%s-*)' % '-*'.join('A' * nargs)
+
+        # if this is an optional action, -- is not allowed
+        if action.option_strings:
+            nargs_pattern = nargs_pattern.replace('-*', '')
+            nargs_pattern = nargs_pattern.replace('-', '')
+
+        # return the pattern
+        return nargs_pattern
+
+    # ========================
+    # Value conversion methods
+    # ========================
+    def _get_values(self, action, arg_strings):
+        # for everything but PARSER args, strip out '--'
+        if action.nargs not in [PARSER, REMAINDER]:
+            arg_strings = [s for s in arg_strings if s != '--']
+
+        # optional argument produces a default when not present
+        if not arg_strings and action.nargs == OPTIONAL:
+            if action.option_strings:
+                value = action.const
+            else:
+                value = action.default
+            if isinstance(value, basestring):
+                value = self._get_value(action, value)
+                self._check_value(action, value)
+
+        # when nargs='*' on a positional, if there were no command-line
+        # args, use the default if it is anything other than None
+        elif (not arg_strings and action.nargs == ZERO_OR_MORE and
+              not action.option_strings):
+            if action.default is not None:
+                value = action.default
+            else:
+                value = arg_strings
+            self._check_value(action, value)
+
+        # single argument or optional argument produces a single value
+        elif len(arg_strings) == 1 and action.nargs in [None, OPTIONAL]:
+            arg_string, = arg_strings
+            value = self._get_value(action, arg_string)
+            self._check_value(action, value)
+
+        # REMAINDER arguments convert all values, checking none
+        elif action.nargs == REMAINDER:
+            value = [self._get_value(action, v) for v in arg_strings]
+
+        # PARSER arguments convert all values, but check only the first
+        elif action.nargs == PARSER:
+            value = [self._get_value(action, v) for v in arg_strings]
+            self._check_value(action, value[0])
+
+        # all other types of nargs produce a list
+        else:
+            value = [self._get_value(action, v) for v in arg_strings]
+            for v in value:
+                self._check_value(action, v)
+
+        # return the converted value
+        return value
+
+    def _get_value(self, action, arg_string):
+        type_func = self._registry_get('type', action.type, action.type)
+        if not _callable(type_func):
+            msg = _('%r is not callable')
+            raise ArgumentError(action, msg % type_func)
+
+        # convert the value to the appropriate type
+        try:
+            result = type_func(arg_string)
+
+        # ArgumentTypeErrors indicate errors
+        except ArgumentTypeError:
+            name = getattr(action.type, '__name__', repr(action.type))
+            msg = str(_sys.exc_info()[1])
+            raise ArgumentError(action, msg)
+
+        # TypeErrors or ValueErrors also indicate errors
+        except (TypeError, ValueError):
+            name = getattr(action.type, '__name__', repr(action.type))
+            msg = _('invalid %s value: %r')
+            raise ArgumentError(action, msg % (name, arg_string))
+
+        # return the converted value
+        return result
+
+    def _check_value(self, action, value):
+        # converted value must be one of the choices (if specified)
+        if action.choices is not None and value not in action.choices:
+            tup = value, ', '.join(map(repr, action.choices))
+            msg = _('invalid choice: %r (choose from %s)') % tup
+            raise ArgumentError(action, msg)
+
+    # =======================
+    # Help-formatting methods
+    # =======================
+    def format_usage(self):
+        formatter = self._get_formatter()
+        formatter.add_usage(self.usage, self._actions,
+                            self._mutually_exclusive_groups)
+        return formatter.format_help()
+
+    def format_help(self):
+        formatter = self._get_formatter()
+
+        # usage
+        formatter.add_usage(self.usage, self._actions,
+                            self._mutually_exclusive_groups)
+
+        # description
+        formatter.add_text(self.description)
+
+        # positionals, optionals and user-defined groups
+        for action_group in self._action_groups:
+            formatter.start_section(action_group.title)
+            formatter.add_text(action_group.description)
+            formatter.add_arguments(action_group._group_actions)
+            formatter.end_section()
+
+        # epilog
+        formatter.add_text(self.epilog)
+
+        # determine help from format above
+        return formatter.format_help()
+
+    def format_version(self):
+        import warnings
+        warnings.warn(
+            'The format_version method is deprecated -- the "version" '
+            'argument to ArgumentParser is no longer supported.',
+            DeprecationWarning)
+        formatter = self._get_formatter()
+        formatter.add_text(self.version)
+        return formatter.format_help()
+
+    def _get_formatter(self):
+        return self.formatter_class(prog=self.prog)
+
+    # =====================
+    # Help-printing methods
+    # =====================
+    def print_usage(self, file=None):
+        if file is None:
+            file = _sys.stdout
+        self._print_message(self.format_usage(), file)
+
+    def print_help(self, file=None):
+        if file is None:
+            file = _sys.stdout
+        self._print_message(self.format_help(), file)
+
+    def print_version(self, file=None):
+        import warnings
+        warnings.warn(
+            'The print_version method is deprecated -- the "version" '
+            'argument to ArgumentParser is no longer supported.',
+            DeprecationWarning)
+        self._print_message(self.format_version(), file)
+
+    def _print_message(self, message, file=None):
+        if message:
+            if file is None:
+                file = _sys.stderr
+            file.write(message)
+
+    # ===============
+    # Exiting methods
+    # ===============
+    def exit(self, status=0, message=None):
+        if message:
+            self._print_message(message, _sys.stderr)
+        _sys.exit(status)
+
+    def error(self, message):
+        """error(message: string)
+
+        Prints a usage message incorporating the message to stderr and
+        exits.
+
+        If you override this in a subclass, it should not return -- it
+        should either exit or raise an exception.
+        """
+        self.print_usage(_sys.stderr)
+        self.exit(2, _('%s: error: %s\n') % (self.prog, message))
diff --git a/lib/spack/spack/cmd/checksum.py b/lib/spack/spack/cmd/checksum.py
index f5cf0d0143c..5a8109b70f2 100644
--- a/lib/spack/spack/cmd/checksum.py
+++ b/lib/spack/spack/cmd/checksum.py
@@ -24,7 +24,7 @@
 ##############################################################################
 import os
 import re
-import argparse
+from external import argparse
 import hashlib
 from pprint import pprint
 from subprocess import CalledProcessError
diff --git a/lib/spack/spack/cmd/clean.py b/lib/spack/spack/cmd/clean.py
index 6091cae6c8e..1df9d87ae26 100644
--- a/lib/spack/spack/cmd/clean.py
+++ b/lib/spack/spack/cmd/clean.py
@@ -22,7 +22,7 @@
 # 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
+from external import argparse
 
 import llnl.util.tty as tty
 
diff --git a/lib/spack/spack/cmd/compiler.py b/lib/spack/spack/cmd/compiler.py
index a4cd2df7e2f..ac9c844a4c8 100644
--- a/lib/spack/spack/cmd/compiler.py
+++ b/lib/spack/spack/cmd/compiler.py
@@ -22,7 +22,7 @@
 # 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
+from external import argparse
 
 import llnl.util.tty as tty
 from llnl.util.tty.colify import colify
diff --git a/lib/spack/spack/cmd/config.py b/lib/spack/spack/cmd/config.py
index 85f96420197..283bfc19b9f 100644
--- a/lib/spack/spack/cmd/config.py
+++ b/lib/spack/spack/cmd/config.py
@@ -23,7 +23,7 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
-import argparse
+from external import argparse
 
 import llnl.util.tty as tty
 
diff --git a/lib/spack/spack/cmd/dependents.py b/lib/spack/spack/cmd/dependents.py
index 129a4eeb237..652f243b988 100644
--- a/lib/spack/spack/cmd/dependents.py
+++ b/lib/spack/spack/cmd/dependents.py
@@ -22,7 +22,7 @@
 # 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
+from external import argparse
 
 import llnl.util.tty as tty
 
diff --git a/lib/spack/spack/cmd/dotkit.py b/lib/spack/spack/cmd/dotkit.py
index 7a691ae5c04..efd442aa763 100644
--- a/lib/spack/spack/cmd/dotkit.py
+++ b/lib/spack/spack/cmd/dotkit.py
@@ -25,7 +25,7 @@
 import sys
 import os
 import shutil
-import argparse
+from external import argparse
 
 import llnl.util.tty as tty
 from llnl.util.lang import partition_list
diff --git a/lib/spack/spack/cmd/fetch.py b/lib/spack/spack/cmd/fetch.py
index 1dd8703daf2..0ccebd9486f 100644
--- a/lib/spack/spack/cmd/fetch.py
+++ b/lib/spack/spack/cmd/fetch.py
@@ -22,7 +22,7 @@
 # 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
+from external import argparse
 
 import spack
 import spack.cmd
diff --git a/lib/spack/spack/cmd/find.py b/lib/spack/spack/cmd/find.py
index 72df69d18a8..2238484a216 100644
--- a/lib/spack/spack/cmd/find.py
+++ b/lib/spack/spack/cmd/find.py
@@ -24,7 +24,7 @@
 ##############################################################################
 import sys
 import collections
-import argparse
+from external import argparse
 from StringIO import StringIO
 
 import llnl.util.tty as tty
diff --git a/lib/spack/spack/cmd/install.py b/lib/spack/spack/cmd/install.py
index 4570d6c40f4..2374d02feba 100644
--- a/lib/spack/spack/cmd/install.py
+++ b/lib/spack/spack/cmd/install.py
@@ -23,7 +23,7 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
-import argparse
+from external import argparse
 
 import spack
 import spack.cmd
diff --git a/lib/spack/spack/cmd/mirror.py b/lib/spack/spack/cmd/mirror.py
index 129ac6bd459..a039e3383a3 100644
--- a/lib/spack/spack/cmd/mirror.py
+++ b/lib/spack/spack/cmd/mirror.py
@@ -24,10 +24,10 @@
 ##############################################################################
 import os
 import shutil
-import argparse
 from datetime import datetime
 from contextlib import closing
 
+from external import argparse
 import llnl.util.tty as tty
 from llnl.util.tty.colify import colify
 from llnl.util.filesystem import mkdirp, join_path
diff --git a/lib/spack/spack/cmd/patch.py b/lib/spack/spack/cmd/patch.py
index 2356583b074..a6556c4828c 100644
--- a/lib/spack/spack/cmd/patch.py
+++ b/lib/spack/spack/cmd/patch.py
@@ -22,7 +22,7 @@
 # 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
+from external import argparse
 
 import spack.cmd
 import spack
diff --git a/lib/spack/spack/cmd/providers.py b/lib/spack/spack/cmd/providers.py
index 1a652c82d17..2bcdc9fba2a 100644
--- a/lib/spack/spack/cmd/providers.py
+++ b/lib/spack/spack/cmd/providers.py
@@ -23,7 +23,7 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-import argparse
+from external import argparse
 
 from llnl.util.tty.colify import colify
 
diff --git a/lib/spack/spack/cmd/python.py b/lib/spack/spack/cmd/python.py
index 641394044c1..86b8c827f8f 100644
--- a/lib/spack/spack/cmd/python.py
+++ b/lib/spack/spack/cmd/python.py
@@ -25,7 +25,7 @@
 import os
 import sys
 import code
-import argparse
+from external import argparse
 import platform
 from contextlib import closing
 
diff --git a/lib/spack/spack/cmd/spec.py b/lib/spack/spack/cmd/spec.py
index fb5a900c3f9..5fcb0a9b5aa 100644
--- a/lib/spack/spack/cmd/spec.py
+++ b/lib/spack/spack/cmd/spec.py
@@ -22,7 +22,7 @@
 # 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
+from external import argparse
 import spack.cmd
 
 import llnl.util.tty as tty
diff --git a/lib/spack/spack/cmd/stage.py b/lib/spack/spack/cmd/stage.py
index 1bf1f93c2fb..2673cdc2661 100644
--- a/lib/spack/spack/cmd/stage.py
+++ b/lib/spack/spack/cmd/stage.py
@@ -22,7 +22,7 @@
 # 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
+from external import argparse
 
 import spack
 import spack.cmd
diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index 73c98a203ba..84eb4703a68 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -22,7 +22,7 @@
 # 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
+from external import argparse
 
 import llnl.util.tty as tty
 
diff --git a/lib/spack/spack/cmd/unuse.py b/lib/spack/spack/cmd/unuse.py
index a31e16d11ad..5d586ccd28f 100644
--- a/lib/spack/spack/cmd/unuse.py
+++ b/lib/spack/spack/cmd/unuse.py
@@ -22,7 +22,7 @@
 # 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
+from external import argparse
 import spack.cmd.use
 
 description ="Remove package from environment using dotkit."
diff --git a/lib/spack/spack/cmd/use.py b/lib/spack/spack/cmd/use.py
index 10a0644df82..029a51801c6 100644
--- a/lib/spack/spack/cmd/use.py
+++ b/lib/spack/spack/cmd/use.py
@@ -22,7 +22,7 @@
 # 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
+from external import argparse
 import llnl.util.tty as tty
 import spack
 
diff --git a/lib/spack/spack/relations.py b/lib/spack/spack/relations.py
index a7b46cfb331..5afb7e7624d 100644
--- a/lib/spack/spack/relations.py
+++ b/lib/spack/spack/relations.py
@@ -72,7 +72,6 @@ class Mpileaks(Package):
 
 import re
 import inspect
-import importlib
 
 from llnl.util.lang import *
 

From 5a5da817a1041b57cc4ae0f2ee16ee0d75701c57 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 10 Aug 2014 11:52:17 -0700
Subject: [PATCH 35/71] Fix SPACK-27 & remove dependence on check_output

- subprocess.check_output is python 2.7 only
- Spack checks for existence of requested prefix, creates it if it does not exist.
---
 lib/spack/spack/cmd/bootstrap.py | 25 +++++++++++++++++--------
 1 file changed, 17 insertions(+), 8 deletions(-)

diff --git a/lib/spack/spack/cmd/bootstrap.py b/lib/spack/spack/cmd/bootstrap.py
index 31c908d42b7..f75b68b00ac 100644
--- a/lib/spack/spack/cmd/bootstrap.py
+++ b/lib/spack/spack/cmd/bootstrap.py
@@ -23,12 +23,13 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-from subprocess import check_call, check_output
+from subprocess import check_call
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import join_path
+from llnl.util.filesystem import join_path, mkdirp
 
 import spack
+from spack.util.executable import which
 
 description = "Create a new installation of spack in another prefix"
 
@@ -38,8 +39,10 @@ def setup_parser(subparser):
 
 def get_origin_url():
     git_dir = join_path(spack.prefix, '.git')
-    origin_url = check_output(
-        ['git', '--git-dir=%s' % git_dir, 'config', '--get', 'remote.origin.url'])
+    git = which('git', required=True)
+    origin_url = git(
+        '--git-dir=%s' % git_dir, 'config', '--get', 'remote.origin.url',
+        return_output=True)
     return origin_url.strip()
 
 
@@ -49,6 +52,11 @@ def bootstrap(parser, args):
 
     tty.msg("Fetching spack from origin: %s" % origin_url)
 
+    if os.path.isfile(prefix):
+        tty.die("There is already a file at %s" % prefix)
+
+    mkdirp(prefix)
+
     if os.path.exists(join_path(prefix, '.git')):
         tty.die("There already seems to be a git repository in %s" % prefix)
 
@@ -62,10 +70,11 @@ def bootstrap(parser, args):
             "%s/lib/spack/..." % prefix)
 
     os.chdir(prefix)
-    check_call(['git', 'init', '--shared', '-q'])
-    check_call(['git', 'remote', 'add', 'origin', origin_url])
-    check_call(['git', 'fetch', 'origin', 'master:refs/remotes/origin/master', '-n', '-q'])
-    check_call(['git', 'reset', '--hard', 'origin/master', '-q'])
+    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('reset', '--hard', 'origin/master', '-q')
 
     tty.msg("Successfully created a new spack in %s" % prefix,
             "Run %s/bin/spack to use this installation." % prefix)

From a41a19d14db7108c141e5737c5acdbbdda201af8 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 10 Aug 2014 16:04:41 -0700
Subject: [PATCH 36/71] Change dict comprehensions to dict() constructors.

---
 lib/spack/spack/compiler.py           | 2 +-
 lib/spack/spack/compilers/__init__.py | 2 +-
 lib/spack/spack/package.py            | 2 +-
 lib/spack/spack/util/crypto.py        | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/spack/spack/compiler.py b/lib/spack/spack/compiler.py
index 716356bdd2a..582f49eaf28 100644
--- a/lib/spack/spack/compiler.py
+++ b/lib/spack/spack/compiler.py
@@ -189,7 +189,7 @@ def check(key):
                 return None
 
         successful = [key for key in parmap(check, checks) if key is not None]
-        return { (v, p, s) : path for v, p, s, path in successful }
+        return dict(((v, p, s), path) for v, p, s, path in successful)
 
     @classmethod
     def find(cls, *path):
diff --git a/lib/spack/spack/compilers/__init__.py b/lib/spack/spack/compilers/__init__.py
index c5bfe21ed43..467472cced5 100644
--- a/lib/spack/spack/compilers/__init__.py
+++ b/lib/spack/spack/compilers/__init__.py
@@ -176,7 +176,7 @@ def compilers_for_spec(compiler_spec):
     config = _get_config()
 
     def get_compiler(cspec):
-        items = { k:v for k,v in config.items('compiler "%s"' % cspec) }
+        items = dict((k,v) for k,v in config.items('compiler "%s"' % cspec))
 
         if not all(n in items for n in _required_instance_vars):
             raise InvalidCompilerConfigurationError(cspec)
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 8df658e6603..b0a9dd76b97 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -360,7 +360,7 @@ def sanity_check_dict(attr_name):
 
         # Version-ize the keys in versions dict
         try:
-            self.versions = { Version(v):h for v,h in self.versions.items() }
+            self.versions = dict((Version(v), h) for v,h in self.versions.items())
         except ValueError:
             raise ValueError("Keys of versions dict in package %s must be versions!"
                              % self.name)
diff --git a/lib/spack/spack/util/crypto.py b/lib/spack/spack/util/crypto.py
index 4d8681bed95..950e8075969 100644
--- a/lib/spack/spack/util/crypto.py
+++ b/lib/spack/spack/util/crypto.py
@@ -35,7 +35,7 @@
     hashlib.sha512 ]
 
 """Index for looking up hasher for a digest."""
-_size_to_hash = { h().digest_size : h for h in _acceptable_hashes }
+_size_to_hash = dict((h().digest_size, h) for h in _acceptable_hashes)
 
 
 def checksum(hashlib_algo, filename, **kwargs):

From ca328a69935e5ed315caaec6d1435e4924e6ee63 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 10 Aug 2014 17:52:46 -0700
Subject: [PATCH 37/71] Fix minor warning about Exception.message being
 deprecated.

---
 lib/spack/spack/error.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/spack/spack/error.py b/lib/spack/spack/error.py
index 40e0e75fdb4..8bcbd83c288 100644
--- a/lib/spack/spack/error.py
+++ b/lib/spack/spack/error.py
@@ -28,7 +28,8 @@ class SpackError(Exception):
        Subclasses can be found in the modules they have to do with.
     """
     def __init__(self, message, long_message=None):
-        super(SpackError, self).__init__(message)
+        super(SpackError, self).__init__()
+        self.message = message
         self.long_message = long_message
 
 

From d86a6380993edfe498bcd6c7d71b2cfff2ef986b Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 10 Aug 2014 17:54:39 -0700
Subject: [PATCH 38/71] Add Python 2.7 functools.total_ordering to external
 modules.

- removing dependence on 2.7
- added it to pyqver2 ads well
---
 lib/spack/external/functools.py | 30 ++++++++++++++++++++++++++++++
 lib/spack/external/pyqver2.py   |  1 +
 lib/spack/spack/version.py      |  3 ++-
 3 files changed, 33 insertions(+), 1 deletion(-)
 create mode 100644 lib/spack/external/functools.py

diff --git a/lib/spack/external/functools.py b/lib/spack/external/functools.py
new file mode 100644
index 00000000000..19f0903c822
--- /dev/null
+++ b/lib/spack/external/functools.py
@@ -0,0 +1,30 @@
+#
+# Backport of Python 2.7's total_ordering.
+#
+
+def total_ordering(cls):
+    """Class decorator that fills in missing ordering methods"""
+    convert = {
+        '__lt__': [('__gt__', lambda self, other: not (self < other or self == other)),
+                   ('__le__', lambda self, other: self < other or self == other),
+                   ('__ge__', lambda self, other: not self < other)],
+        '__le__': [('__ge__', lambda self, other: not self <= other or self == other),
+                   ('__lt__', lambda self, other: self <= other and not self == other),
+                   ('__gt__', lambda self, other: not self <= other)],
+        '__gt__': [('__lt__', lambda self, other: not (self > other or self == other)),
+                   ('__ge__', lambda self, other: self > other or self == other),
+                   ('__le__', lambda self, other: not self > other)],
+        '__ge__': [('__le__', lambda self, other: (not self >= other) or self == other),
+                   ('__gt__', lambda self, other: self >= other and not self == other),
+                   ('__lt__', lambda self, other: not self >= other)]
+    }
+    roots = set(dir(cls)) & set(convert)
+    if not roots:
+        raise ValueError('must define at least one ordering operation: < > <= >=')
+    root = max(roots)       # prefer __lt__ to __le__ to __gt__ to __ge__
+    for opname, opfunc in convert[root]:
+        if opname not in roots:
+            opfunc.__name__ = opname
+            opfunc.__doc__ = getattr(int, opname).__doc__
+            setattr(cls, opname, opfunc)
+    return cls
diff --git a/lib/spack/external/pyqver2.py b/lib/spack/external/pyqver2.py
index 875f8837fb9..cd45bf948f8 100755
--- a/lib/spack/external/pyqver2.py
+++ b/lib/spack/external/pyqver2.py
@@ -114,6 +114,7 @@
     "collections.Counter":      (2, 7),
     "collections.defaultdict":  (2, 5),
     "collections.OrderedDict":  (2, 7),
+    "functools.total_ordering": (2, 7),
     "enumerate":                (2, 3),
     "frozenset":                (2, 4),
     "itertools.compress":       (2, 7),
diff --git a/lib/spack/spack/version.py b/lib/spack/spack/version.py
index 4558f883843..fbf86db8e18 100644
--- a/lib/spack/spack/version.py
+++ b/lib/spack/spack/version.py
@@ -47,7 +47,8 @@
 import sys
 import re
 from bisect import bisect_left
-from functools import total_ordering, wraps
+from functools import wraps
+from external.functools import total_ordering
 
 import llnl.util.compare.none_high as none_high
 import llnl.util.compare.none_low as none_low

From d95e7ecfe1ea7bb84c5b4f1e2e59045b0d89e34e Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 10 Aug 2014 17:56:36 -0700
Subject: [PATCH 39/71] Remove dependency on Python2.7 OrderedDict, revise
 config parser

---
 lib/spack/external/ordereddict.py | 262 ++++++++++++++++++++++++++++++
 lib/spack/spack/config.py         |  66 +++-----
 2 files changed, 284 insertions(+), 44 deletions(-)
 create mode 100644 lib/spack/external/ordereddict.py

diff --git a/lib/spack/external/ordereddict.py b/lib/spack/external/ordereddict.py
new file mode 100644
index 00000000000..8ddad1477ea
--- /dev/null
+++ b/lib/spack/external/ordereddict.py
@@ -0,0 +1,262 @@
+#
+# Backport of OrderedDict() class that runs on Python 2.4, 2.5, 2.6, 2.7 and pypy.
+# Passes Python2.7's test suite and incorporates all the latest updates.
+#
+# From http://code.activestate.com/recipes/576693-ordered-dictionary-for-py24/
+# This file is in the public domain, and has no particular license.
+#
+try:
+    from thread import get_ident as _get_ident
+except ImportError:
+    from dummy_thread import get_ident as _get_ident
+
+try:
+    from _abcoll import KeysView, ValuesView, ItemsView
+except ImportError:
+    pass
+
+
+class OrderedDict(dict):
+    'Dictionary that remembers insertion order'
+    # An inherited dict maps keys to values.
+    # The inherited dict provides __getitem__, __len__, __contains__, and get.
+    # The remaining methods are order-aware.
+    # Big-O running times for all methods are the same as for regular dictionaries.
+
+    # The internal self.__map dictionary maps keys to links in a doubly linked list.
+    # The circular doubly linked list starts and ends with a sentinel element.
+    # The sentinel element never gets deleted (this simplifies the algorithm).
+    # Each link is stored as a list of length three:  [PREV, NEXT, KEY].
+
+    def __init__(self, *args, **kwds):
+        '''Initialize an ordered dictionary.  Signature is the same as for
+        regular dictionaries, but keyword arguments are not recommended
+        because their insertion order is arbitrary.
+
+        '''
+        if len(args) > 1:
+            raise TypeError('expected at most 1 arguments, got %d' % len(args))
+        try:
+            self.__root
+        except AttributeError:
+            self.__root = root = []                     # sentinel node
+            root[:] = [root, root, None]
+            self.__map = {}
+        self.__update(*args, **kwds)
+
+    def __setitem__(self, key, value, dict_setitem=dict.__setitem__):
+        'od.__setitem__(i, y) <==> od[i]=y'
+        # Setting a new item creates a new link which goes at the end of the linked
+        # list, and the inherited dictionary is updated with the new key/value pair.
+        if key not in self:
+            root = self.__root
+            last = root[0]
+            last[1] = root[0] = self.__map[key] = [last, root, key]
+        dict_setitem(self, key, value)
+
+    def __delitem__(self, key, dict_delitem=dict.__delitem__):
+        'od.__delitem__(y) <==> del od[y]'
+        # Deleting an existing item uses self.__map to find the link which is
+        # then removed by updating the links in the predecessor and successor nodes.
+        dict_delitem(self, key)
+        link_prev, link_next, key = self.__map.pop(key)
+        link_prev[1] = link_next
+        link_next[0] = link_prev
+
+    def __iter__(self):
+        'od.__iter__() <==> iter(od)'
+        root = self.__root
+        curr = root[1]
+        while curr is not root:
+            yield curr[2]
+            curr = curr[1]
+
+    def __reversed__(self):
+        'od.__reversed__() <==> reversed(od)'
+        root = self.__root
+        curr = root[0]
+        while curr is not root:
+            yield curr[2]
+            curr = curr[0]
+
+    def clear(self):
+        'od.clear() -> None.  Remove all items from od.'
+        try:
+            for node in self.__map.itervalues():
+                del node[:]
+            root = self.__root
+            root[:] = [root, root, None]
+            self.__map.clear()
+        except AttributeError:
+            pass
+        dict.clear(self)
+
+    def popitem(self, last=True):
+        '''od.popitem() -> (k, v), return and remove a (key, value) pair.
+        Pairs are returned in LIFO order if last is true or FIFO order if false.
+
+        '''
+        if not self:
+            raise KeyError('dictionary is empty')
+        root = self.__root
+        if last:
+            link = root[0]
+            link_prev = link[0]
+            link_prev[1] = root
+            root[0] = link_prev
+        else:
+            link = root[1]
+            link_next = link[1]
+            root[1] = link_next
+            link_next[0] = root
+        key = link[2]
+        del self.__map[key]
+        value = dict.pop(self, key)
+        return key, value
+
+    # -- the following methods do not depend on the internal structure --
+
+    def keys(self):
+        'od.keys() -> list of keys in od'
+        return list(self)
+
+    def values(self):
+        'od.values() -> list of values in od'
+        return [self[key] for key in self]
+
+    def items(self):
+        'od.items() -> list of (key, value) pairs in od'
+        return [(key, self[key]) for key in self]
+
+    def iterkeys(self):
+        'od.iterkeys() -> an iterator over the keys in od'
+        return iter(self)
+
+    def itervalues(self):
+        'od.itervalues -> an iterator over the values in od'
+        for k in self:
+            yield self[k]
+
+    def iteritems(self):
+        'od.iteritems -> an iterator over the (key, value) items in od'
+        for k in self:
+            yield (k, self[k])
+
+    def update(*args, **kwds):
+        '''od.update(E, **F) -> None.  Update od from dict/iterable E and F.
+
+        If E is a dict instance, does:           for k in E: od[k] = E[k]
+        If E has a .keys() method, does:         for k in E.keys(): od[k] = E[k]
+        Or if E is an iterable of items, does:   for k, v in E: od[k] = v
+        In either case, this is followed by:     for k, v in F.items(): od[k] = v
+
+        '''
+        if len(args) > 2:
+            raise TypeError('update() takes at most 2 positional '
+                            'arguments (%d given)' % (len(args),))
+        elif not args:
+            raise TypeError('update() takes at least 1 argument (0 given)')
+        self = args[0]
+        # Make progressively weaker assumptions about "other"
+        other = ()
+        if len(args) == 2:
+            other = args[1]
+        if isinstance(other, dict):
+            for key in other:
+                self[key] = other[key]
+        elif hasattr(other, 'keys'):
+            for key in other.keys():
+                self[key] = other[key]
+        else:
+            for key, value in other:
+                self[key] = value
+        for key, value in kwds.items():
+            self[key] = value
+
+    __update = update  # let subclasses override update without breaking __init__
+
+    __marker = object()
+
+    def pop(self, key, default=__marker):
+        '''od.pop(k[,d]) -> v, remove specified key and return the corresponding value.
+        If key is not found, d is returned if given, otherwise KeyError is raised.
+
+        '''
+        if key in self:
+            result = self[key]
+            del self[key]
+            return result
+        if default is self.__marker:
+            raise KeyError(key)
+        return default
+
+    def setdefault(self, key, default=None):
+        'od.setdefault(k[,d]) -> od.get(k,d), also set od[k]=d if k not in od'
+        if key in self:
+            return self[key]
+        self[key] = default
+        return default
+
+    def __repr__(self, _repr_running={}):
+        'od.__repr__() <==> repr(od)'
+        call_key = id(self), _get_ident()
+        if call_key in _repr_running:
+            return '...'
+        _repr_running[call_key] = 1
+        try:
+            if not self:
+                return '%s()' % (self.__class__.__name__,)
+            return '%s(%r)' % (self.__class__.__name__, self.items())
+        finally:
+            del _repr_running[call_key]
+
+    def __reduce__(self):
+        'Return state information for pickling'
+        items = [[k, self[k]] for k in self]
+        inst_dict = vars(self).copy()
+        for k in vars(OrderedDict()):
+            inst_dict.pop(k, None)
+        if inst_dict:
+            return (self.__class__, (items,), inst_dict)
+        return self.__class__, (items,)
+
+    def copy(self):
+        'od.copy() -> a shallow copy of od'
+        return self.__class__(self)
+
+    @classmethod
+    def fromkeys(cls, iterable, value=None):
+        '''OD.fromkeys(S[, v]) -> New ordered dictionary with keys from S
+        and values equal to v (which defaults to None).
+
+        '''
+        d = cls()
+        for key in iterable:
+            d[key] = value
+        return d
+
+    def __eq__(self, other):
+        '''od.__eq__(y) <==> od==y.  Comparison to another OD is order-sensitive
+        while comparison to a regular mapping is order-insensitive.
+
+        '''
+        if isinstance(other, OrderedDict):
+            return len(self)==len(other) and self.items() == other.items()
+        return dict.__eq__(self, other)
+
+    def __ne__(self, other):
+        return not self == other
+
+    # -- the following methods are only used in Python 2.7 --
+
+    def viewkeys(self):
+        "od.viewkeys() -> a set-like object providing a view on od's keys"
+        return KeysView(self)
+
+    def viewvalues(self):
+        "od.viewvalues() -> an object providing a view on od's values"
+        return ValuesView(self)
+
+    def viewitems(self):
+        "od.viewitems() -> a set-like object providing a view on od's items"
+        return ItemsView(self)
diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 5494adc324a..85ee16a1c20 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -84,10 +84,9 @@
 import re
 import inspect
 import ConfigParser as cp
-from collections import OrderedDict
 
+from external.ordereddict import OrderedDict
 from llnl.util.lang import memoized
-
 import spack.error
 
 __all__ = [
@@ -222,7 +221,6 @@ class SpackConfigParser(cp.RawConfigParser):
     """
     # Slightly modify Python option expressions to allow leading whitespace
     OPTCRE    = re.compile(r'\s*' + cp.RawConfigParser.OPTCRE.pattern)
-    OPTCRE_NV = re.compile(r'\s*' + cp.RawConfigParser.OPTCRE_NV.pattern)
 
     def __init__(self, file_or_files):
         cp.RawConfigParser.__init__(self, dict_type=OrderedDict)
@@ -341,14 +339,13 @@ def write(self, path_or_fp=None):
 
 
     def _read(self, fp, fpname):
-        """This is a copy of Python 2.7's _read() method, with support for
-           continuation lines removed.
-        """
-        cursect = None                        # None, or a dictionary
+        """This is a copy of Python 2.6's _read() method, with support for
+           continuation lines removed."""
+        cursect = None                            # None, or a dictionary
         optname = None
-        lineno = 0
         comment = 0
-        e = None                              # None, or an exception
+        lineno = 0
+        e = None                                  # None, or an exception
         while True:
             line = fp.readline()
             if not line:
@@ -359,7 +356,6 @@ def _read(self, fp, fpname):
                 (line.split(None, 1)[0].lower() == 'rem' and line[0] in "rR")):
                 self._sections["comment-%d" % comment] = line
                 comment += 1
-                continue
             # a section header or option header?
             else:
                 # is it a section header?
@@ -381,27 +377,21 @@ def _read(self, fp, fpname):
                     raise cp.MissingSectionHeaderError(fpname, lineno, line)
                 # an option line?
                 else:
-                    mo = self._optcre.match(line)
+                    mo = self.OPTCRE.match(line)
                     if mo:
                         optname, vi, optval = mo.group('option', 'vi', 'value')
+                        if vi in ('=', ':') and ';' in optval:
+                            # ';' is a comment delimiter only if it follows
+                            # a spacing character
+                            pos = optval.find(';')
+                            if pos != -1 and optval[pos-1].isspace():
+                                optval = optval[:pos]
+                        optval = optval.strip()
+                        # allow empty values
+                        if optval == '""':
+                            optval = ''
                         optname = self.optionxform(optname.rstrip())
-                        # This check is fine because the OPTCRE cannot
-                        # match if it would set optval to None
-                        if optval is not None:
-                            if vi in ('=', ':') and ';' in optval:
-                                # ';' is a comment delimiter only if it follows
-                                # a spacing character
-                                pos = optval.find(';')
-                                if pos != -1 and optval[pos-1].isspace():
-                                    optval = optval[:pos]
-                            optval = optval.strip()
-                            # allow empty values
-                            if optval == '""':
-                                optval = ''
-                            cursect[optname] = [optval]
-                        else:
-                            # valueless option handling
-                            cursect[optname] = optval
+                        cursect[optname] = optval
                     else:
                         # a non-fatal parsing error occurred.  set up the
                         # exception but keep going. the exception will be
@@ -414,23 +404,13 @@ def _read(self, fp, fpname):
         if e:
             raise e
 
-        # join the multi-line values collected while reading
-        all_sections = [self._defaults]
-        all_sections.extend(self._sections.values())
-        for options in all_sections:
-            # skip comments
-            if isinstance(options, basestring):
-                continue
 
-            for name, val in options.items():
-                if isinstance(val, list):
-                    options[name] = '\n'.join(val)
 
 
     def _write(self, fp):
         """Write an .ini-format representation of the configuration state.
 
-           This is taken from the default Python 2.7 source.  It writes 4
+           This is taken from the default Python 2.6 source.  It writes 4
            spaces at the beginning of lines instead of no leading space.
         """
         if self._defaults:
@@ -449,11 +429,9 @@ def _write(self, fp):
                 # Allow leading whitespace
                 fp.write("[%s]\n" % section)
                 for (key, value) in self._sections[section].items():
-                    if key == "__name__":
-                        continue
-                    if (value is not None) or (self._optcre == self.OPTCRE):
-                        key = " = ".join((key, str(value).replace('\n', '\n\t')))
-                    fp.write("    %s\n" % (key))
+                    if key != "__name__":
+                        fp.write("    %s = %s\n" %
+                                 (key, str(value).replace('\n', '\n\t')))
 
 
 class SpackConfigurationError(spack.error.SpackError):

From 696e80c62f548c71220fe37545f6ff7abc3f4e22 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 10 Aug 2014 17:57:10 -0700
Subject: [PATCH 40/71] Get rid of Python 2.7 dict.viewkeys() call.

---
 lib/spack/spack/spec.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index aa6397271b7..4838fd99466 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -838,7 +838,7 @@ def normalize(self, **kwargs):
 
         # If there are deps specified but not visited, they're not
         # actually deps of this package.  Raise an error.
-        extra = set(spec_deps.viewkeys()).difference(visited)
+        extra = set(spec_deps.keys()).difference(visited)
 
         # Also subtract out all the packags that provide a needed vpkg
         vdeps = [v for v in self.package.virtual_dependencies()]

From 7082b0a59af0eb71fcf1c3165da1505197d488e9 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 10 Aug 2014 18:05:13 -0700
Subject: [PATCH 41/71] cc supports Python 2.6

---
 lib/spack/env/cc                       | 6 +++---
 lib/spack/spack/test/python_version.py | 1 +
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 9e71d25cafb..266e41cb486 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -1,12 +1,11 @@
 #!/usr/bin/env python
 import sys
-if not sys.version_info[:2] >= (2,7):
-    sys.exit("Spack requires Python 2.7.  Version was %s." % sys.version_info)
+if not sys.version_info[:2] >= (2,6):
+    sys.exit("Spack requires Python 2.6.  Version was %s." % sys.version_info)
 
 import os
 import re
 import subprocess
-import argparse
 from contextlib import closing
 
 # Import spack parameters through the build environment.
@@ -18,6 +17,7 @@ if not spack_lib:
 # Grab a minimal set of spack packages
 sys.path.append(spack_lib)
 from spack.compilation import *
+from external import argparse
 import llnl.util.tty as tty
 
 spack_prefix        = get_env_var("SPACK_PREFIX")
diff --git a/lib/spack/spack/test/python_version.py b/lib/spack/spack/test/python_version.py
index f814df32261..04b4eadf345 100644
--- a/lib/spack/spack/test/python_version.py
+++ b/lib/spack/spack/test/python_version.py
@@ -45,6 +45,7 @@ class PythonVersionTest(unittest.TestCase):
     def spack_python_files(self):
         # first file is the spack script.
         yield spack.spack_file
+        yield os.path.join(spack.build_env_path, 'cc')
 
         # Next files are all the source files and package files.
         search_paths = [spack.lib_path, spack.var_path]

From 48d5281e3a9142ded1e67983a22dce3f5777e1b4 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 10 Aug 2014 18:00:20 -0700
Subject: [PATCH 42/71] Test cases pass; Spack supports Python 2.6!

---
 bin/spack                                  |   4 +-
 lib/spack/spack/stage.py                   |   3 +-
 lib/spack/spack/test/__init__.py           |   4 +-
 lib/spack/spack/test/concretize.py         |  24 ++--
 lib/spack/spack/test/mock_packages_test.py |   3 +-
 lib/spack/spack/test/spec_dag.py           |  46 ++++----
 lib/spack/spack/test/stage.py              | 122 +++++++++++----------
 7 files changed, 104 insertions(+), 102 deletions(-)

diff --git a/bin/spack b/bin/spack
index 0af8d62b5e2..679ca9f1be0 100755
--- a/bin/spack
+++ b/bin/spack
@@ -24,8 +24,8 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
-if not sys.version_info[:2] >= (2,7):
-    sys.exit("Spack requires Python 2.7.  Version was %s." % sys.version_info)
+if not sys.version_info[:2] >= (2,6):
+    sys.exit("Spack requires Python 2.6.  Version was %s." % sys.version_info)
 
 import os
 
diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py
index 839555d6303..3dac7983963 100644
--- a/lib/spack/spack/stage.py
+++ b/lib/spack/spack/stage.py
@@ -120,8 +120,7 @@ def _need_to_create_path(self):
             if spack.use_tmp_stage:
                 # If we're using a tmp dir, it's a link, and it points at the right spot,
                 # then keep it.
-                if (os.path.commonprefix((real_path, real_tmp)) == real_tmp
-                    and os.path.exists(real_path)):
+                if (real_path.startswith(real_tmp) and os.path.exists(real_path)):
                     return False
                 else:
                     # otherwise, just unlink it and start over.
diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py
index 4479c45d770..8ddc7f227d8 100644
--- a/lib/spack/spack/test/__init__.py
+++ b/lib/spack/spack/test/__init__.py
@@ -72,7 +72,7 @@ def run(names, verbose=False):
 
     runner = unittest.TextTestRunner(verbosity=verbosity)
 
-    testsRun = errors = failures = skipped = 0
+    testsRun = errors = failures = 0
     for test in names:
         module = 'spack.test.' + test
         print module
@@ -83,12 +83,10 @@ def run(names, verbose=False):
         testsRun += result.testsRun
         errors   += len(result.errors)
         failures += len(result.failures)
-        skipped  += len(result.skipped)
 
     succeeded = not errors and not failures
     tty.msg("Tests Complete.",
             "%5d tests run" % testsRun,
-            "%5d skipped" % skipped,
             "%5d failures" % failures,
             "%5d errors" % errors)
 
diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py
index 6ad2ef29d8d..a7f4812c8cf 100644
--- a/lib/spack/spack/test/concretize.py
+++ b/lib/spack/spack/test/concretize.py
@@ -134,29 +134,29 @@ def test_concretize_with_provides_when(self):
     def test_virtual_is_fully_expanded_for_callpath(self):
         # force dependence on fake "zmpi" by asking for MPI 10.0
         spec = Spec('callpath ^mpi@10.0')
-        self.assertIn('mpi', spec.dependencies)
-        self.assertNotIn('fake', spec)
+        self.assertTrue('mpi' in spec.dependencies)
+        self.assertFalse('fake' in spec)
 
         spec.concretize()
 
-        self.assertIn('zmpi', spec.dependencies)
-        self.assertNotIn('mpi', spec)
-        self.assertIn('fake', spec.dependencies['zmpi'])
+        self.assertTrue('zmpi' in spec.dependencies)
+        self.assertFalse('mpi' in spec)
+        self.assertTrue('fake' in spec.dependencies['zmpi'])
 
 
     def test_virtual_is_fully_expanded_for_mpileaks(self):
         spec = Spec('mpileaks ^mpi@10.0')
-        self.assertIn('mpi', spec.dependencies)
-        self.assertNotIn('fake', spec)
+        self.assertTrue('mpi' in spec.dependencies)
+        self.assertFalse('fake' in spec)
 
         spec.concretize()
 
-        self.assertIn('zmpi', spec.dependencies)
-        self.assertIn('callpath', spec.dependencies)
-        self.assertIn('zmpi', spec.dependencies['callpath'].dependencies)
-        self.assertIn('fake', spec.dependencies['callpath'].dependencies['zmpi'].dependencies)
+        self.assertTrue('zmpi' in spec.dependencies)
+        self.assertTrue('callpath' in spec.dependencies)
+        self.assertTrue('zmpi' in spec.dependencies['callpath'].dependencies)
+        self.assertTrue('fake' in spec.dependencies['callpath'].dependencies['zmpi'].dependencies)
 
-        self.assertNotIn('mpi', spec)
+        self.assertFalse('mpi' in spec)
 
 
     def test_my_dep_depends_on_provider_of_my_virtual_dep(self):
diff --git a/lib/spack/spack/test/mock_packages_test.py b/lib/spack/spack/test/mock_packages_test.py
index adde70ff6c2..e9483760393 100644
--- a/lib/spack/spack/test/mock_packages_test.py
+++ b/lib/spack/spack/test/mock_packages_test.py
@@ -39,7 +39,6 @@ def set_pkg_dep(pkg, spec):
 
 
 class MockPackagesTest(unittest.TestCase):
-    @classmethod
     def setUp(self):
         # Use the mock packages database for these tests.  This allows
         # us to set up contrived packages that don't interfere with
@@ -52,7 +51,7 @@ def setUp(self):
             'site' : spack.mock_site_config,
             'user' : spack.mock_user_config }
 
-    @classmethod
+
     def tearDown(self):
         """Restore the real packages path after any test."""
         spack.db = self.real_db
diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py
index 322f34cf024..fb67aa8a8da 100644
--- a/lib/spack/spack/test/spec_dag.py
+++ b/lib/spack/spack/test/spec_dag.py
@@ -57,10 +57,10 @@ def test_preorder_node_traversal(self):
         pairs = zip([0,1,2,3,4,2,3], names)
 
         traversal = dag.traverse()
-        self.assertListEqual([x.name for x in traversal], names)
+        self.assertEqual([x.name for x in traversal], names)
 
         traversal = dag.traverse(depth=True)
-        self.assertListEqual([(x, y.name) for x,y in traversal], pairs)
+        self.assertEqual([(x, y.name) for x,y in traversal], pairs)
 
 
     def test_preorder_edge_traversal(self):
@@ -72,10 +72,10 @@ def test_preorder_edge_traversal(self):
         pairs = zip([0,1,2,3,4,3,2,3,1], names)
 
         traversal = dag.traverse(cover='edges')
-        self.assertListEqual([x.name for x in traversal], names)
+        self.assertEqual([x.name for x in traversal], names)
 
         traversal = dag.traverse(cover='edges', depth=True)
-        self.assertListEqual([(x, y.name) for x,y in traversal], pairs)
+        self.assertEqual([(x, y.name) for x,y in traversal], pairs)
 
 
     def test_preorder_path_traversal(self):
@@ -87,10 +87,10 @@ def test_preorder_path_traversal(self):
         pairs = zip([0,1,2,3,4,3,2,3,1,2], names)
 
         traversal = dag.traverse(cover='paths')
-        self.assertListEqual([x.name for x in traversal], names)
+        self.assertEqual([x.name for x in traversal], names)
 
         traversal = dag.traverse(cover='paths', depth=True)
-        self.assertListEqual([(x, y.name) for x,y in traversal], pairs)
+        self.assertEqual([(x, y.name) for x,y in traversal], pairs)
 
 
     def test_postorder_node_traversal(self):
@@ -102,10 +102,10 @@ def test_postorder_node_traversal(self):
         pairs = zip([4,3,2,3,2,1,0], names)
 
         traversal = dag.traverse(order='post')
-        self.assertListEqual([x.name for x in traversal], names)
+        self.assertEqual([x.name for x in traversal], names)
 
         traversal = dag.traverse(depth=True, order='post')
-        self.assertListEqual([(x, y.name) for x,y in traversal], pairs)
+        self.assertEqual([(x, y.name) for x,y in traversal], pairs)
 
 
     def test_postorder_edge_traversal(self):
@@ -117,10 +117,10 @@ def test_postorder_edge_traversal(self):
         pairs = zip([4,3,3,2,3,2,1,1,0], names)
 
         traversal = dag.traverse(cover='edges', order='post')
-        self.assertListEqual([x.name for x in traversal], names)
+        self.assertEqual([x.name for x in traversal], names)
 
         traversal = dag.traverse(cover='edges', depth=True, order='post')
-        self.assertListEqual([(x, y.name) for x,y in traversal], pairs)
+        self.assertEqual([(x, y.name) for x,y in traversal], pairs)
 
 
     def test_postorder_path_traversal(self):
@@ -132,10 +132,10 @@ def test_postorder_path_traversal(self):
         pairs = zip([4,3,3,2,3,2,1,2,1,0], names)
 
         traversal = dag.traverse(cover='paths', order='post')
-        self.assertListEqual([x.name for x in traversal], names)
+        self.assertEqual([x.name for x in traversal], names)
 
         traversal = dag.traverse(cover='paths', depth=True, order='post')
-        self.assertListEqual([(x, y.name) for x,y in traversal], pairs)
+        self.assertEqual([(x, y.name) for x,y in traversal], pairs)
 
 
     def test_conflicting_spec_constraints(self):
@@ -199,13 +199,13 @@ def test_normalize_with_virtual_spec(self):
     def check_links(self, spec_to_check):
         for spec in spec_to_check.traverse():
             for dependent in spec.dependents.values():
-                self.assertIn(
-                    spec.name, dependent.dependencies,
+                self.assertTrue(
+                    spec.name in dependent.dependencies,
                     "%s not in dependencies of %s" % (spec.name, dependent.name))
 
             for dependency in spec.dependencies.values():
-                self.assertIn(
-                    spec.name, dependency.dependents,
+                self.assertTrue(
+                    spec.name in dependency.dependents,
                     "%s not in dependents of %s" % (spec.name, dependency.name))
 
 
@@ -385,13 +385,13 @@ def test_normalize_with_virtual_package(self):
 
     def test_contains(self):
         spec = Spec('mpileaks ^mpi ^libelf@1.8.11 ^libdwarf')
-        self.assertIn(Spec('mpi'), spec)
-        self.assertIn(Spec('libelf'), spec)
-        self.assertIn(Spec('libelf@1.8.11'), spec)
-        self.assertNotIn(Spec('libelf@1.8.12'), spec)
-        self.assertIn(Spec('libdwarf'), spec)
-        self.assertNotIn(Spec('libgoblin'), spec)
-        self.assertIn(Spec('mpileaks'), spec)
+        self.assertTrue(Spec('mpi') in spec)
+        self.assertTrue(Spec('libelf') in spec)
+        self.assertTrue(Spec('libelf@1.8.11') in spec)
+        self.assertFalse(Spec('libelf@1.8.12') in spec)
+        self.assertTrue(Spec('libdwarf') in spec)
+        self.assertFalse(Spec('libgoblin') in spec)
+        self.assertTrue(Spec('mpileaks') in spec)
 
 
     def test_copy_simple(self):
diff --git a/lib/spack/spack/test/stage.py b/lib/spack/spack/test/stage.py
index 08899f98105..a412549dc71 100644
--- a/lib/spack/spack/test/stage.py
+++ b/lib/spack/spack/test/stage.py
@@ -51,28 +51,20 @@
 stage_name = 'spack-test-stage'
 
 
-class with_tmp(object):
-    """Decorator that executes a function with or without spack set to use
-       a temp dir.  Spack allows builds to happen directly in the
-       stage directory or in a tmp dir and symlinked into the stage
-       directory, so this lets us use the same test in both cases.
+@contextmanager
+def use_tmp(use_tmp):
+    """Allow some test code to be executed with spack.use_tmp_stage
+       set to a certain value.  Context manager makes sure it's reset
+       on failure.
     """
-    def __init__(self, use_tmp):
-        self.use_tmp = use_tmp
-
-    def __call__(self, fun):
-        use_tmp = self.use_tmp
-        def new_test_function(self):
-            old_tmp = spack.use_tmp_stage
-            spack.use_tmp_stage = use_tmp
-            fun(self)
-            spack.use_tmp_stage = old_tmp
-        return new_test_function
+    old_tmp = spack.use_tmp_stage
+    spack.use_tmp_stage = use_tmp
+    yield
+    spack.use_tmp_stage = old_tmp
 
 
 class StageTest(unittest.TestCase):
-    @classmethod
-    def setUpClass(cls):
+    def setUp(self):
         """This sets up a mock archive to fetch, and a mock temp space for use
            by the Stage class.  It doesn't actually create the Stage -- that
            is done by individual tests.
@@ -92,52 +84,58 @@ def setUpClass(cls):
             tar('czf', archive_name, archive_dir)
 
         # Make spack use the test environment for tmp stuff.
-        cls.old_tmp_dirs = spack.tmp_dirs
+        self.old_tmp_dirs = spack.tmp_dirs
         spack.tmp_dirs = [test_tmp_path]
 
+        # record this since this test changes to directories that will
+        # be removed.
+        self.working_dir = os.getcwd()
 
-    @classmethod
-    def tearDownClass(cls):
+
+    def tearDown(self):
         """Blows away the test environment directory."""
         shutil.rmtree(test_files_dir)
 
+        # chdir back to original working dir
+        os.chdir(self.working_dir)
+
         # restore spack's original tmp environment
-        spack.tmp_dirs = cls.old_tmp_dirs
+        spack.tmp_dirs = self.old_tmp_dirs
 
 
     def get_stage_path(self, stage, stage_name):
-        """Figure out based on a stage and an intended name where it should
-           be living.  This depends on whether it's named or not.
+        """Figure out where a stage should be living.  This depends on
+           whether it's named.
         """
-        if stage_name:
+        if stage_name is not None:
             # If it is a named stage, we know where the stage should be
-            stage_path = join_path(spack.stage_path, stage_name)
+            return join_path(spack.stage_path, stage_name)
         else:
             # If it's unnamed, ensure that we ran mkdtemp in the right spot.
-            stage_path = stage.path
-            self.assertIsNotNone(stage_path)
-            self.assertEqual(
-                os.path.commonprefix((stage_path, spack.stage_path)),
-                spack.stage_path)
-        return stage_path
+            self.assertTrue(stage.path is not None)
+            self.assertTrue(stage.path.startswith(spack.stage_path))
+            return stage.path
 
 
     def check_setup(self, stage, stage_name):
         """Figure out whether a stage was set up correctly."""
         stage_path = self.get_stage_path(stage, stage_name)
+
+        # Ensure stage was created in the spack stage directory
         self.assertTrue(os.path.isdir(stage_path))
 
         if spack.use_tmp_stage:
-            # Make sure everything was created and linked correctly for
-            # a tmp stage.
+            # Check that the stage dir is really a symlink.
             self.assertTrue(os.path.islink(stage_path))
 
+            # Make sure it points to a valid directory
             target = os.path.realpath(stage_path)
             self.assertTrue(os.path.isdir(target))
             self.assertFalse(os.path.islink(target))
-            self.assertEqual(
-                os.path.commonprefix((target, test_tmp_path)),
-                test_tmp_path)
+
+            # Make sure the directory is in the place we asked it to
+            # be (see setUp and tearDown)
+            self.assertTrue(target.startswith(test_tmp_path))
 
         else:
             # Make sure the stage path is NOT a link for a non-tmp stage
@@ -146,15 +144,15 @@ def check_setup(self, stage, stage_name):
 
     def check_fetch(self, stage, stage_name):
         stage_path = self.get_stage_path(stage, stage_name)
-        self.assertIn(archive_name, os.listdir(stage_path))
+        self.assertTrue(archive_name in os.listdir(stage_path))
         self.assertEqual(join_path(stage_path, archive_name),
                          stage.archive_file)
 
 
     def check_expand_archive(self, stage, stage_name):
         stage_path = self.get_stage_path(stage, stage_name)
-        self.assertIn(archive_name, os.listdir(stage_path))
-        self.assertIn(archive_dir, os.listdir(stage_path))
+        self.assertTrue(archive_name in os.listdir(stage_path))
+        self.assertTrue(archive_dir in os.listdir(stage_path))
 
         self.assertEqual(
             join_path(stage_path, archive_dir),
@@ -192,32 +190,40 @@ def check_destroy(self, stage, stage_name):
             self.assertFalse(os.path.exists(target))
 
 
-    def checkSetupAndDestroy(self, stage_name=None):
-        stage = Stage(archive_url, name=stage_name)
-        self.check_setup(stage, stage_name)
-
-        stage.destroy()
-        self.check_destroy(stage, stage_name)
-
-
-    @with_tmp(True)
     def test_setup_and_destroy_name_with_tmp(self):
-        self.checkSetupAndDestroy(stage_name)
+        with use_tmp(True):
+            stage = Stage(archive_url, name=stage_name)
+            self.check_setup(stage, stage_name)
+
+            stage.destroy()
+            self.check_destroy(stage, stage_name)
 
 
-    @with_tmp(False)
     def test_setup_and_destroy_name_without_tmp(self):
-        self.checkSetupAndDestroy(stage_name)
+        with use_tmp(False):
+            stage = Stage(archive_url, name=stage_name)
+            self.check_setup(stage, stage_name)
+
+            stage.destroy()
+            self.check_destroy(stage, stage_name)
 
 
-    @with_tmp(True)
     def test_setup_and_destroy_no_name_with_tmp(self):
-        self.checkSetupAndDestroy(None)
+        with use_tmp(True):
+            stage = Stage(archive_url)
+            self.check_setup(stage, None)
+
+            stage.destroy()
+            self.check_destroy(stage, None)
 
 
-    @with_tmp(False)
     def test_setup_and_destroy_no_name_without_tmp(self):
-        self.checkSetupAndDestroy(None)
+        with use_tmp(False):
+            stage = Stage(archive_url)
+            self.check_setup(stage, None)
+
+            stage.destroy()
+            self.check_destroy(stage, None)
 
 
     def test_chdir(self):
@@ -286,7 +292,7 @@ def test_restage(self):
         with closing(open('foobar', 'w')) as file:
             file.write("this file is to be destroyed.")
 
-        self.assertIn('foobar', os.listdir(stage.expanded_archive_path))
+        self.assertTrue('foobar' in os.listdir(stage.expanded_archive_path))
 
         # Make sure the file is not there after restage.
         stage.restage()
@@ -295,7 +301,7 @@ def test_restage(self):
 
         stage.chdir_to_archive()
         self.check_chdir_to_archive(stage, stage_name)
-        self.assertNotIn('foobar', os.listdir(stage.expanded_archive_path))
+        self.assertFalse('foobar' in os.listdir(stage.expanded_archive_path))
 
         stage.destroy()
         self.check_destroy(stage, stage_name)

From 113afe860ecea247c5ed343b814a633565c2033b Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 10 Jul 2014 15:52:24 -0700
Subject: [PATCH 43/71] More robust symbol inclusion for 'from spack import *'

- avoid errors where some symbols aren't exported to packages.
- reduce the number of places each symbol needs to be mentioned in
  an __all__ list
---
 lib/spack/spack/__init__.py | 41 +++++++++++++++++++++----------------
 1 file changed, 23 insertions(+), 18 deletions(-)

diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py
index 9eae4342e3b..a3f00a11b18 100644
--- a/lib/spack/spack/__init__.py
+++ b/lib/spack/spack/__init__.py
@@ -22,20 +22,6 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-
-#
-# When packages call 'from spack import *', this is what is brought in.
-#
-# Spack internal code calls 'import spack' and accesses other
-# variables (spack.db, paths, etc.) directly.
-#
-# TODO: maybe this should be separated out and should go in build_environment.py?
-# TODO: it's not clear where all the stuff that needs to be included in packages
-#       should live.  This file is overloaded for spack core vs. for packages.
-__all__ = ['Package', 'when', 'provides', 'depends_on', 'version',
-           'patch', 'Version', 'working_dir', 'which', 'Executable',
-           'filter_file', 'change_sed_delimiter']
-
 import os
 import tempfile
 from llnl.util.filesystem import *
@@ -141,11 +127,30 @@
 #
 sys_type = None
 
+
 #
-# Extra imports that should be generally usable from package.py files.
+# When packages call 'from spack import *', this extra stuff is brought in.
 #
-from llnl.util.filesystem import working_dir
+# Spack internal code should call 'import spack' and accesses other
+# variables (spack.db, paths, etc.) directly.
+#
+# TODO: maybe this should be separated out and should go in build_environment.py?
+# TODO: it's not clear where all the stuff that needs to be included in packages
+#       should live.  This file is overloaded for spack core vs. for packages.
+#
+__all__ = ['Package', 'Version', 'when']
 from spack.package import Package
-from spack.relations import *
-from spack.multimethod import when
 from spack.version import Version
+from spack.multimethod import when
+
+import llnl.util.filesystem
+from llnl.util.filesystem import *
+__all__ += llnl.util.filesystem.__all__
+
+import spack.relations
+from spack.relations import *
+__all__ += spack.relations.__all__
+
+import spack.util.executable
+from spack.util.executable import *
+__all__ += spack.util.executable.__all__

From 0bba101ff90f317c81385306c8beaaacbaa62759 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 10 Jul 2014 15:53:31 -0700
Subject: [PATCH 44/71] Allow packages to add a dotkit() method and write
 custom parts of dotkits.

---
 lib/spack/spack/hooks/dotkit.py | 32 +++++++++++++++++++++++++++-----
 1 file changed, 27 insertions(+), 5 deletions(-)

diff --git a/lib/spack/spack/hooks/dotkit.py b/lib/spack/spack/hooks/dotkit.py
index 10b77323534..524145e6c15 100644
--- a/lib/spack/spack/hooks/dotkit.py
+++ b/lib/spack/spack/hooks/dotkit.py
@@ -33,6 +33,23 @@
 import spack
 
 
+class DotkitFile(object):
+    def __init__(self, path):
+        self.dk_file = open(path, 'w')
+
+    def close(self):
+        self.dk_file.close()
+
+    def write(self, *args):
+        self.dk_file.write(*args)
+
+    def alter(self, var, path):
+        self.dk_file.write("dk_alter %s %s\n" % (var, path))
+
+    def setenv(self, var, value):
+        self.dk_file.write("dk_setenv %s %s\n" % (var, value))
+
+
 def dotkit_file(pkg):
     dk_file_name = pkg.spec.format('$_$@$%@$+$=$#') + ".dk"
     return join_path(spack.dotkit_path, dk_file_name)
@@ -51,15 +68,15 @@ def post_install(pkg):
         ('LD_LIBRARY_PATH', pkg.prefix.lib64)]:
 
         if os.path.isdir(path):
-            alterations.append("dk_alter %s %s\n" % (var, path))
+            alterations.append((var, path))
 
     if not alterations:
         return
 
-    alterations.append("dk_alter CMAKE_PREFIX_PATH %s\n" % pkg.prefix)
+    alterations.append(("CMAKE_PREFIX_PATH", pkg.prefix))
 
     dk_file = dotkit_file(pkg)
-    with closing(open(dk_file, 'w')) as dk:
+    with closing(DotkitFile(dk_file)) as dk:
         # Put everything in the spack category.
         dk.write('#c spack\n')
 
@@ -72,8 +89,13 @@ def post_install(pkg):
                 dk.write("#h %s\n" % line)
 
         # Write alterations
-        for alter in alterations:
-            dk.write(alter)
+        for alt in alterations:
+            dk.alter(*alt)
+
+        # callback in case package has extensions.
+        dotkit_fun = getattr(pkg, 'dotkit', None)
+        if dotkit_fun and hasattr(dotkit_fun, '__call__'):
+            dotkit_fun(dk)
 
 
 def post_uninstall(pkg):

From 0740c576a714281b0449e33f1b8e4b00e5d9d9c0 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 10 Jul 2014 15:54:10 -0700
Subject: [PATCH 45/71] Package for postgresql.

---
 var/spack/packages/postgresql/package.py | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 var/spack/packages/postgresql/package.py

diff --git a/var/spack/packages/postgresql/package.py b/var/spack/packages/postgresql/package.py
new file mode 100644
index 00000000000..bf14c3b922a
--- /dev/null
+++ b/var/spack/packages/postgresql/package.py
@@ -0,0 +1,24 @@
+from spack import *
+
+class Postgresql(Package):
+    """PostgreSQL is a powerful, open source object-relational
+       database system. It has more than 15 years of active
+       development and a proven architecture that has earned it a
+       strong reputation for reliability, data integrity, and
+       correctness."""
+    homepage = "http://www.postgresql.org/"
+    url      = "http://ftp.postgresql.org/pub/source/v9.3.4/postgresql-9.3.4.tar.bz2"
+
+    version('9.3.4', 'd0a41f54c377b2d2fab4a003b0dac762')
+
+    def install(self, spec, prefix):
+        # FIXME: Modify the configure line to suit your build system here.
+        configure("--prefix=%s" % prefix)
+
+        # FIXME: Add logic to build and install here
+        make()
+        make("install")
+
+
+    def dotkit(self, dk):
+        dk.setenv('PGDATA', "%s/data" %self.prefix)

From 5a3803de39a67a42a70b4048039c77c4831633b2 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Fri, 25 Jul 2014 19:38:48 -0700
Subject: [PATCH 46/71] Add options to stage to make it just print out stage
 dir.

---
 lib/spack/spack/cmd/stage.py | 42 ++++++++++++++++++++++++++++++------
 1 file changed, 36 insertions(+), 6 deletions(-)

diff --git a/lib/spack/spack/cmd/stage.py b/lib/spack/spack/cmd/stage.py
index 1bf1f93c2fb..7b21faa721d 100644
--- a/lib/spack/spack/cmd/stage.py
+++ b/lib/spack/spack/cmd/stage.py
@@ -23,6 +23,9 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
+import os
+
+import llnl.util.tty as tty
 
 import spack
 import spack.cmd
@@ -33,18 +36,45 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-n', '--no-checksum', action='store_true', dest='no_checksum',
         help="Do not check downloaded packages against checksum")
+
+    dir_parser = subparser.add_mutually_exclusive_group()
+    dir_parser.add_argument(
+        '-d', '--stage-dir', action='store_const', dest='print_dir',
+        const='stage', help="Prints out the stage directory for a spec.")
+    dir_parser.add_argument(
+        '-b', '--build-dir', action='store_const', dest='print_dir',
+        const='build', help="Prints out the expanded archive path for a spec.")
+
     subparser.add_argument(
-        'packages', nargs=argparse.REMAINDER, help="specs of packages to stage")
+        'specs', nargs=argparse.REMAINDER, help="specs of packages to stage")
 
 
 def stage(parser, args):
-    if not args.packages:
+    if not args.specs:
         tty.die("stage requires at least one package argument")
 
     if args.no_checksum:
         spack.do_checksum = False
 
-    specs = spack.cmd.parse_specs(args.packages, concretize=True)
-    for spec in specs:
-        package = spack.db.get(spec)
-        package.do_stage()
+    specs = spack.cmd.parse_specs(args.specs, concretize=True)
+
+    if args.print_dir:
+        if len(specs) != 1:
+            tty.die("--stage-dir and --build-dir options only take one spec.")
+
+        spec = specs[0]
+        pkg = spack.db.get(spec)
+
+        if args.print_dir == 'stage':
+            print pkg.stage.path
+        elif args.print_dir == 'build':
+            if not os.listdir(pkg.stage.path):
+                tty.die("Stage directory is empty.  Run this first:",
+                        "spack stage " + " ".join(args.specs))
+            print pkg.stage.expanded_archive_path
+
+    else:
+        for spec in specs:
+            package = spack.db.get(spec)
+            package.do_stage()
+

From abc7d401e2d411642a9cc2b1de96990da2d17c63 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Fri, 25 Jul 2014 19:39:10 -0700
Subject: [PATCH 47/71] Add "spack cd" shell support to cd directly into the
 staged archive.

---
 share/spack/setup-env.bash | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/share/spack/setup-env.bash b/share/spack/setup-env.bash
index e22a2591672..53c53dfee55 100755
--- a/share/spack/setup-env.bash
+++ b/share/spack/setup-env.bash
@@ -65,6 +65,10 @@ function spack {
     # Filter out use and unuse.  For any other commands, just run the
     # command.
     case $_spack_subcommand in
+        "cd")
+            cd $(spack stage -b "$@")
+            return
+            ;;
         "use") ;;
         "unuse") ;;
         *)

From 0b68d1292d9b415b74abc63e909c44399ae9a97a Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Fri, 25 Jul 2014 20:07:05 -0700
Subject: [PATCH 48/71] Add package for openssl, have postgres use it.

- Updated version wildcard to include [a-z]|alpha|beta
  to accommodate all the letter suffixes on openssl.
---
 var/spack/packages/openssl/package.py    | 26 ++++++++++++++++++++++++
 var/spack/packages/postgresql/package.py |  8 ++++----
 2 files changed, 30 insertions(+), 4 deletions(-)
 create mode 100644 var/spack/packages/openssl/package.py

diff --git a/var/spack/packages/openssl/package.py b/var/spack/packages/openssl/package.py
new file mode 100644
index 00000000000..c5a8aeb9dc2
--- /dev/null
+++ b/var/spack/packages/openssl/package.py
@@ -0,0 +1,26 @@
+from spack import *
+
+class Openssl(Package):
+    """The OpenSSL Project is a collaborative effort to develop a
+       robust, commercial-grade, full-featured, and Open Source
+       toolkit implementing the Secure Sockets Layer (SSL v2/v3) and
+       Transport Layer Security (TLS v1) protocols as well as a
+       full-strength general purpose cryptography library."""
+    homepage = "http://www.openssl.org"
+    url      = "http://www.openssl.org/source/openssl-1.0.1h.tar.gz"
+
+    version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf')
+
+    depends_on("zlib")
+    parallel = False
+
+    def install(self, spec, prefix):
+        config = Executable("./config")
+        config("--prefix=%s" % prefix,
+               "--openssldir=%s/etc/openssl" % prefix,
+               "zlib",
+               "no-krb5",
+               "shared")
+
+        make()
+        make("install")
diff --git a/var/spack/packages/postgresql/package.py b/var/spack/packages/postgresql/package.py
index bf14c3b922a..a93f87df804 100644
--- a/var/spack/packages/postgresql/package.py
+++ b/var/spack/packages/postgresql/package.py
@@ -11,11 +11,11 @@ class Postgresql(Package):
 
     version('9.3.4', 'd0a41f54c377b2d2fab4a003b0dac762')
 
-    def install(self, spec, prefix):
-        # FIXME: Modify the configure line to suit your build system here.
-        configure("--prefix=%s" % prefix)
+    depends_on("openssl")
 
-        # FIXME: Add logic to build and install here
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix,
+                  "--with-openssl")
         make()
         make("install")
 

From 90cd0c7efa9cc6b1e58530bede25deeaaaf9f52e Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 31 Jul 2014 13:26:55 -0700
Subject: [PATCH 49/71] Add Kevin's experimental TAU version

---
 var/spack/packages/tau/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/packages/tau/package.py b/var/spack/packages/tau/package.py
index 8d9dbe1759b..33320622db2 100644
--- a/var/spack/packages/tau/package.py
+++ b/var/spack/packages/tau/package.py
@@ -11,7 +11,8 @@ class Tau(Package):
     url      = "http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/tau-2.23.1.tar.gz"
 
     version('2.23.1', '6593b47ae1e7a838e632652f0426fe72')
-
+    version('2.23-perfdb', 'c97b404bcd94c7d9b04fa3dc0a32b0d1',
+            url='http://www.nic.uoregon.edu/~khuck/tau2-latest.tar.gz')
 
     def install(self, spec, prefix):
         # TAU isn't happy with directories that have '@' in the path.  Sigh.

From 6127b0baa69fa469cf9a02dcd5dc78f674b746b3 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 6 Aug 2014 21:58:59 -0700
Subject: [PATCH 50/71] new prototype TAU tarball from Kevin

---
 var/spack/packages/tau/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/packages/tau/package.py b/var/spack/packages/tau/package.py
index 33320622db2..e58acfb41a4 100644
--- a/var/spack/packages/tau/package.py
+++ b/var/spack/packages/tau/package.py
@@ -10,8 +10,8 @@ class Tau(Package):
     homepage = "http://www.cs.uoregon.edu/research/tau"
     url      = "http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/tau-2.23.1.tar.gz"
 
-    version('2.23.1', '6593b47ae1e7a838e632652f0426fe72')
-    version('2.23-perfdb', 'c97b404bcd94c7d9b04fa3dc0a32b0d1',
+    version('2.23.1',        '6593b47ae1e7a838e632652f0426fe72')
+    version('2.23.2-perfdb', 'f743a65951220f5b46b9d3cf179129d0',
             url='http://www.nic.uoregon.edu/~khuck/tau2-latest.tar.gz')
 
     def install(self, spec, prefix):

From fa3b19000db9ed6f3d6cf31895aeee4ac0d4e633 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 11 Aug 2014 22:47:13 -0700
Subject: [PATCH 51/71] update tau tarball

---
 var/spack/packages/tau/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/packages/tau/package.py b/var/spack/packages/tau/package.py
index e58acfb41a4..caafe4e2c92 100644
--- a/var/spack/packages/tau/package.py
+++ b/var/spack/packages/tau/package.py
@@ -11,7 +11,7 @@ class Tau(Package):
     url      = "http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/tau-2.23.1.tar.gz"
 
     version('2.23.1',        '6593b47ae1e7a838e632652f0426fe72')
-    version('2.23.2-perfdb', 'f743a65951220f5b46b9d3cf179129d0',
+    version('2.23.2-perfdb', '4048f693eee246d48eb2619c0f05999e',
             url='http://www.nic.uoregon.edu/~khuck/tau2-latest.tar.gz')
 
     def install(self, spec, prefix):

From 221cf6acb932442f5964243eb3413a1d921920c8 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 16 Aug 2014 14:53:57 -0700
Subject: [PATCH 52/71] Consolidate most module code into spack.modules and
 spack.cmd.module

- One file with all the module classes (spack/modules.py)
  - Has an EnvModule superclass that does most of the work and consolidates common code
  - Subclasses have specializations for different module systems (TclModule, Dotkit)

- One command (spack module) for all the types of modules to use
  - the one command is used by the scripts, only need to maintain in one place
  - has some subcommands for different module types, but they're handled mostly generically.

- Consolidate zsh support into a single setup-env.sh script.
---
 bin/spack                                    |   7 +
 lib/spack/spack/__init__.py                  |   2 -
 lib/spack/spack/cmd/load.py                  |  24 +--
 lib/spack/spack/cmd/{dotkit.py => module.py} |  69 +++---
 lib/spack/spack/cmd/tclmodule.py             |  99 ---------
 lib/spack/spack/cmd/unload.py                |   8 +-
 lib/spack/spack/cmd/unuse.py                 |   8 +-
 lib/spack/spack/cmd/use.py                   |  22 +-
 lib/spack/spack/hooks/dotkit.py              |  58 +----
 lib/spack/spack/hooks/tclmodule.py           |  61 +-----
 lib/spack/spack/modules.py                   | 216 +++++++++++++++++++
 share/spack/{setup-env.bash => setup-env.sh} | 115 +++++-----
 share/spack/setup-env.zsh                    | 122 -----------
 13 files changed, 349 insertions(+), 462 deletions(-)
 rename lib/spack/spack/cmd/{dotkit.py => module.py} (60%)
 delete mode 100644 lib/spack/spack/cmd/tclmodule.py
 create mode 100644 lib/spack/spack/modules.py
 rename share/spack/{setup-env.bash => setup-env.sh} (56%)
 delete mode 100755 share/spack/setup-env.zsh

diff --git a/bin/spack b/bin/spack
index c63178b1913..f2b5d1d5838 100755
--- a/bin/spack
+++ b/bin/spack
@@ -75,6 +75,13 @@ for cmd in spack.cmd.commands:
     module = spack.cmd.get_module(cmd)
     subparser = subparsers.add_parser(cmd, help=module.description)
     module.setup_parser(subparser)
+
+# Just print help and exit if run with no arguments at all
+if len(sys.argv) == 1:
+    parser.print_help()
+    sys.exit(1)
+
+# actually parse the args.
 args = parser.parse_args()
 
 # Set up environment based on args.
diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py
index 0b69ccde38f..be38971c309 100644
--- a/lib/spack/spack/__init__.py
+++ b/lib/spack/spack/__init__.py
@@ -58,8 +58,6 @@
 stage_path     = join_path(var_path, "stage")
 install_path   = join_path(prefix, "opt")
 share_path     = join_path(prefix, "share", "spack")
-dotkit_path    = join_path(share_path, "dotkit")
-tclmodule_path    = join_path(share_path, "modules")
 
 #
 # Set up the packages database.
diff --git a/lib/spack/spack/cmd/load.py b/lib/spack/spack/cmd/load.py
index 1389740df15..5bc6b15784c 100644
--- a/lib/spack/spack/cmd/load.py
+++ b/lib/spack/spack/cmd/load.py
@@ -23,28 +23,16 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
-import llnl.util.tty as tty
-import spack
+import spack.modules
 
-description ="Add package to environment using module."
+description ="Add package to environment using modules."
 
 def setup_parser(subparser):
+    """Parser is only constructed so that this prints a nice help
+       message with -h. """
     subparser.add_argument(
-        'spec', nargs=argparse.REMAINDER, help='Spec of package to add.')
-
-
-def print_help():
-    tty.msg("Spack module support is not initialized.",
-            "",
-            "To use module with Spack, you must first run the command",
-            "below, which you can copy and paste:",
-            "",
-            "For bash:",
-            "    . %s/setup-env.bash" % spack.share_path,
-            "",
-            "ksh/csh/tcsh shells are currently unsupported",
-            "")
+        'spec', nargs=argparse.REMAINDER, help='Spec of package to load with modules.')
 
 
 def load(parser, args):
-    print_help()
+    spack.modules.print_help()
diff --git a/lib/spack/spack/cmd/dotkit.py b/lib/spack/spack/cmd/module.py
similarity index 60%
rename from lib/spack/spack/cmd/dotkit.py
rename to lib/spack/spack/cmd/module.py
index 7a691ae5c04..ead3b9abac8 100644
--- a/lib/spack/spack/cmd/dotkit.py
+++ b/lib/spack/spack/cmd/module.py
@@ -32,34 +32,43 @@
 from llnl.util.filesystem import mkdirp
 
 import spack.cmd
-import spack.hooks.dotkit
+import spack.modules
+from spack.util.string import *
+
 from spack.spec import Spec
 
+description ="Manipulate modules and dotkits."
+
+module_types = {
+    'dotkit' : spack.modules.Dotkit,
+    'tcl'    : spack.modules.TclModule
+}
 
-description ="Find dotkits for packages if they exist."
 
 def setup_parser(subparser):
-    subparser.add_argument(
-        '--refresh', action='store_true', help='Regenerate all dotkits')
+    sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='module_command')
 
-    subparser.add_argument(
-        'spec', nargs=argparse.REMAINDER, help='spec to find a dotkit for.')
+    refresh_parser = sp.add_parser('refresh', help='Regenerate all module files.')
+
+    find_parser = sp.add_parser('find', help='Find module files for packages.')
+    find_parser.add_argument(
+        'module_type', help="Type of module to find file for. [" + '|'.join(module_types) + "]")
+    find_parser.add_argument('spec', nargs='+', help='spec to find a module file for.')
 
 
-def dotkit_find(parser, args):
-    if not args.spec:
-        parser.parse_args(['dotkit', '-h'])
-
-    spec = spack.cmd.parse_specs(args.spec)
-    if len(spec) > 1:
+def module_find(mtype, spec_array):
+    specs = spack.cmd.parse_specs(spec_array)
+    if len(specs) > 1:
         tty.die("You can only pass one spec.")
-    spec = spec[0]
+    spec = specs[0]
 
     if not spack.db.exists(spec.name):
         tty.die("No such package: %s" % spec.name)
 
-    specs = [s for s in spack.db.installed_package_specs() if s.satisfies(spec)]
+    if mtype not in module_types:
+        tty.die("Invalid module type: '%s'.  Options are " + comma_and(module_types))
 
+    specs = [s for s in spack.db.installed_package_specs() if s.satisfies(spec)]
     if len(specs) == 0:
         tty.die("No installed packages match spec %s" % spec)
 
@@ -69,31 +78,27 @@ def dotkit_find(parser, args):
             sys.stderr.write(s.tree(color=True))
         sys.exit(1)
 
-    match = specs[0]
-    if not os.path.isfile(spack.hooks.dotkit.dotkit_file(match.package)):
+    mt = module_types[mtype]
+    mod = mt(spec.package)
+    if not os.path.isfile(mod.file_name):
         tty.die("No dotkit is installed for package %s." % spec)
 
-    print match.format('$_$@$+$%@$=$#')
+    print mod.file_name
 
 
-def dotkit_refresh(parser, args):
-    query_specs = spack.cmd.parse_specs(args.spec)
+def module_refresh():
+    shutil.rmtree(spack.dotkit_path, ignore_errors=False)
+    mkdirp(spack.dotkit_path)
 
     specs = spack.db.installed_package_specs()
-    if query_specs:
-        specs = [s for s in specs
-                 if any(s.satisfies(q) for q in query_specs)]
-    else:
-        shutil.rmtree(spack.dotkit_path, ignore_errors=False)
-        mkdirp(spack.dotkit_path)
-
     for spec in specs:
-        spack.hooks.dotkit.post_install(spec.package)
+        for mt in module_types:
+            mt(spec.package).write()
 
 
+def module(parser, args):
+    if args.module_command == 'refresh':
+        module_refresh()
 
-def dotkit(parser, args):
-    if args.refresh:
-        dotkit_refresh(parser, args)
-    else:
-        dotkit_find(parser, args)
+    elif args.module_command == 'find':
+        module_find(args.module_type, args.spec)
diff --git a/lib/spack/spack/cmd/tclmodule.py b/lib/spack/spack/cmd/tclmodule.py
deleted file mode 100644
index 270ee65b7b4..00000000000
--- a/lib/spack/spack/cmd/tclmodule.py
+++ /dev/null
@@ -1,99 +0,0 @@
-##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Written by David Beckingsale, david@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
-# the Free Software Foundation) version 2.1 dated 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 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 sys
-import os
-import shutil
-import argparse
-
-import llnl.util.tty as tty
-from llnl.util.lang import partition_list
-from llnl.util.filesystem import mkdirp
-
-import spack.cmd
-import spack.hooks.tclmodule
-from spack.spec import Spec
-
-
-description ="Find modules for packages if they exist."
-
-def setup_parser(subparser):
-    subparser.add_argument(
-        '--refresh', action='store_true', help='Regenerate all modules')
-
-    subparser.add_argument(
-        'spec', nargs=argparse.REMAINDER, help='spec to find a module for.')
-
-
-def module_find(parser, args):
-    if not args.spec:
-        parser.parse_args(['tclmodule', '-h'])
-
-    spec = spack.cmd.parse_specs(args.spec)
-    if len(spec) > 1:
-        tty.die("You can only pass one spec.")
-    spec = spec[0]
-
-    if not spack.db.exists(spec.name):
-        tty.die("No such package: %s" % spec.name)
-
-    specs = [s for s in spack.db.installed_package_specs() if s.satisfies(spec)]
-
-    if len(specs) == 0:
-        tty.die("No installed packages match spec %s" % spec)
-
-    if len(specs) > 1:
-        tty.error("Multiple matches for spec %s.  Choose one:" % spec)
-        for s in specs:
-            sys.stderr.write(s.tree(color=True))
-        sys.exit(1)
-
-    match = specs[0]
-    if not os.path.isfile(spack.hooks.tclmodule.module_file(match.package)):
-        tty.die("No module is installed for package %s." % spec)
-
-    print match.format('$_$@$+$%@$=$#')
-
-
-def module_refresh(parser, args):
-    query_specs = spack.cmd.parse_specs(args.spec)
-
-    specs = spack.db.installed_package_specs()
-    if query_specs:
-        specs = [s for s in specs
-                 if any(s.satisfies(q) for q in query_specs)]
-    else:
-        shutil.rmtree(spack.tclmodule_path, ignore_errors=False)
-        mkdirp(spack.tclmodule_path)
-
-    for spec in specs:
-        spack.hooks.tclmodule.post_install(spec.package)
-
-
-
-def tclmodule(parser, args):
-    if args.refresh:
-        module_refresh(parser, args)
-    else:
-        module_find(parser, args)
diff --git a/lib/spack/spack/cmd/unload.py b/lib/spack/spack/cmd/unload.py
index df009c840b3..24e49b3f24a 100644
--- a/lib/spack/spack/cmd/unload.py
+++ b/lib/spack/spack/cmd/unload.py
@@ -23,14 +23,16 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
-import spack.cmd.tclmodule
+import spack.modules
 
 description ="Remove package from environment using module."
 
 def setup_parser(subparser):
+    """Parser is only constructed so that this prints a nice help
+       message with -h. """
     subparser.add_argument(
-        'spec', nargs=argparse.REMAINDER, help='Spec of package to remove.')
+        'spec', nargs=argparse.REMAINDER, help='Spec of package to unload with modules.')
 
 
 def unload(parser, args):
-    spack.cmd.load.print_help()
+    spack.modules.print_help()
diff --git a/lib/spack/spack/cmd/unuse.py b/lib/spack/spack/cmd/unuse.py
index a31e16d11ad..7f0b384ea05 100644
--- a/lib/spack/spack/cmd/unuse.py
+++ b/lib/spack/spack/cmd/unuse.py
@@ -23,14 +23,16 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
-import spack.cmd.use
+import spack.modules
 
 description ="Remove package from environment using dotkit."
 
 def setup_parser(subparser):
+    """Parser is only constructed so that this prints a nice help
+       message with -h. """
     subparser.add_argument(
-        'spec', nargs=argparse.REMAINDER, help='Spec of package to remove.')
+        'spec', nargs=argparse.REMAINDER, help='Spec of package to unuse with dotkit.')
 
 
 def unuse(parser, args):
-    spack.cmd.use.print_help()
+    spack.modules.print_help()
diff --git a/lib/spack/spack/cmd/use.py b/lib/spack/spack/cmd/use.py
index 10a0644df82..4990fea2f82 100644
--- a/lib/spack/spack/cmd/use.py
+++ b/lib/spack/spack/cmd/use.py
@@ -23,28 +23,16 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
-import llnl.util.tty as tty
-import spack
+import spack.modules
 
 description ="Add package to environment using dotkit."
 
 def setup_parser(subparser):
+    """Parser is only constructed so that this prints a nice help
+       message with -h. """
     subparser.add_argument(
-        'spec', nargs=argparse.REMAINDER, help='Spec of package to add.')
-
-
-def print_help():
-    tty.msg("Spack dotkit support is not initialized.",
-            "",
-            "To use dotkit with Spack, you must first run the command",
-            "below, which you can copy and paste:",
-            "",
-            "For bash:",
-            "    . %s/setup-env.bash" % spack.share_path,
-            "",
-            "ksh/csh/tcsh shells are currently unsupported",
-            "")
+        'spec', nargs=argparse.REMAINDER, help='Spec of package to use with dotkit.')
 
 
 def use(parser, args):
-    print_help()
+    spack.modules.print_help()
diff --git a/lib/spack/spack/hooks/dotkit.py b/lib/spack/spack/hooks/dotkit.py
index 10b77323534..0f46f6a2fcf 100644
--- a/lib/spack/spack/hooks/dotkit.py
+++ b/lib/spack/spack/hooks/dotkit.py
@@ -22,62 +22,14 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
-import re
-import textwrap
-import shutil
-from contextlib import closing
-
-from llnl.util.filesystem import join_path, mkdirp
-
-import spack
-
-
-def dotkit_file(pkg):
-    dk_file_name = pkg.spec.format('$_$@$%@$+$=$#') + ".dk"
-    return join_path(spack.dotkit_path, dk_file_name)
+import spack.modules
 
 
 def post_install(pkg):
-    if not os.path.exists(spack.dotkit_path):
-        mkdirp(spack.dotkit_path)
-
-    alterations = []
-    for var, path in [
-        ('PATH', pkg.prefix.bin),
-        ('MANPATH', pkg.prefix.man),
-        ('MANPATH', pkg.prefix.share_man),
-        ('LD_LIBRARY_PATH', pkg.prefix.lib),
-        ('LD_LIBRARY_PATH', pkg.prefix.lib64)]:
-
-        if os.path.isdir(path):
-            alterations.append("dk_alter %s %s\n" % (var, path))
-
-    if not alterations:
-        return
-
-    alterations.append("dk_alter CMAKE_PREFIX_PATH %s\n" % pkg.prefix)
-
-    dk_file = dotkit_file(pkg)
-    with closing(open(dk_file, 'w')) as dk:
-        # Put everything in the spack category.
-        dk.write('#c spack\n')
-
-        dk.write('#d %s\n' % pkg.spec.format("$_ $@"))
-
-        # Recycle the description
-        if pkg.__doc__:
-            doc = re.sub(r'\s+', ' ', pkg.__doc__)
-            for line in textwrap.wrap(doc, 72):
-                dk.write("#h %s\n" % line)
-
-        # Write alterations
-        for alter in alterations:
-            dk.write(alter)
+    dk = spack.modules.Dotkit(pkg)
+    dk.write()
 
 
 def post_uninstall(pkg):
-    dk_file = dotkit_file(pkg)
-    if os.path.exists(dk_file):
-        shutil.rmtree(dk_file, ignore_errors=True)
-
+    dk = spack.modules.Dotkit(pkg)
+    dk.remove()
diff --git a/lib/spack/spack/hooks/tclmodule.py b/lib/spack/spack/hooks/tclmodule.py
index d9b4a438319..d93da3177ea 100644
--- a/lib/spack/spack/hooks/tclmodule.py
+++ b/lib/spack/spack/hooks/tclmodule.py
@@ -22,65 +22,14 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
-import re
-import textwrap
-import shutil
-from contextlib import closing
-
-from llnl.util.filesystem import join_path, mkdirp
-
-import spack
-
-
-def module_file(pkg):
-    m_file_name = pkg.spec.format('$_$@$%@$+$=$#')
-    return join_path(spack.tclmodule_path, m_file_name)
+import spack.modules
 
 
 def post_install(pkg):
-    if not os.path.exists(spack.module_path):
-        mkdirp(spack.module_path)
-
-    alterations = []
-    for var, path in [
-        ('PATH', pkg.prefix.bin),
-        ('MANPATH', pkg.prefix.man),
-        ('MANPATH', pkg.prefix.share_man),
-        ('LD_LIBRARY_PATH', pkg.prefix.lib),
-        ('LD_LIBRARY_PATH', pkg.prefix.lib64)]:
-
-        if os.path.isdir(path):
-            alterations.append("prepend-path %s \"%s\"\n" % (var, path))
-
-    if not alterations:
-        return
-
-    alterations.append("prepend-path CMAKE_PREFIX_PATH \"%s\"\n" % pkg.prefix)
-
-    m_file = module_file(pkg)
-    with closing(open(m_file, 'w')) as m:
-        # Put everything in the spack category.
-        m.write('#%Module1.0\n')
-
-        m.write('module-whatis \"%s\"\n\n' % pkg.spec.format("$_ $@"))
-
-        # Recycle the description
-        if pkg.__doc__:
-            m.write('proc ModulesHelp { } {\n')
-            doc = re.sub(r'\s+', ' ', pkg.__doc__)
-            doc = re.sub(r'"', '\"', pkg.__doc__)
-            m.write("puts stderr \"%s\"\n" % doc)
-            m.write('}\n\n')
-
-
-        # Write alterations
-        for alter in alterations:
-            m.write(alter)
+    dk = spack.modules.TclModule(pkg)
+    dk.write()
 
 
 def post_uninstall(pkg):
-    m_file = module_file(pkg)
-    if os.path.exists(m_file):
-        shutil.rmtree(m_file, ignore_errors=True)
-
+    dk = spack.modules.TclModule(pkg)
+    dk.remove()
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
new file mode 100644
index 00000000000..8ac7e470cb5
--- /dev/null
+++ b/lib/spack/spack/modules.py
@@ -0,0 +1,216 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+"""This module contains code for creating environment modules, which
+can include dotkits, tcl modules, lmod, and others.
+
+The various types of modules are installed by post-install hooks and
+removed after an uninstall by post-uninstall hooks.  This class
+consolidates the logic for creating an abstract description of the
+information that module systems need.  Currently that includes a
+number directories to be appended to paths in the user's environment:
+
+  * /bin directories to be appended to PATH
+  * /lib* directories for LD_LIBRARY_PATH
+  * /man* and /share/man* directories for LD_LIBRARY_PATH
+  * the package prefix for CMAKE_PREFIX_PATH
+
+This module also includes logic for coming up with unique names for
+the module files so that they can be found by the various
+shell-support files in $SPACK/share/spack/setup-env.*.
+
+Each hook in hooks/ implements the logic for writing its specific type
+of module file.
+"""
+__all__ = ['EnvModule', 'Dotkit', 'TclModule']
+
+import os
+import re
+import textwrap
+import shutil
+from contextlib import closing
+
+import llnl.util.tty as tty
+from llnl.util.filesystem import join_path, mkdirp
+
+import spack
+
+dotkit_path  = join_path(spack.share_path, "dotkit")
+tcl_mod_path = join_path(spack.share_path, "modules")
+
+def print_help():
+    """For use by commands to tell user how to activate shell support."""
+
+    tty.msg("Spack module/dotkit support is not initialized.",
+            "",
+            "To use dotkit or modules with Spack, you must first run",
+            "one of the commands below.  You can copy/paste them.",
+            "",
+            "For bash and zsh:",
+            "    . %s/setup-env.sh" % spack.share_path,
+            "",
+            "For csh and tcsh:",
+            "    source %s/setup-env.csh" % spack.share_path,
+            "")
+
+
+class EnvModule(object):
+    def __init__(self, pkg=None):
+        # category in the modules system
+        # TODO: come up with smarter category names.
+        self.category = "spack"
+
+        # Descriptions for the module system's UI
+        self.short_description = ""
+        self.long_description = ""
+
+        # dict pathname -> list of directories to be prepended to in
+        # the module file.
+        self._paths = None
+        self.pkg = pkg
+
+
+    @property
+    def paths(self):
+        if self._paths is None:
+            self._paths = {}
+
+            def add_path(self, path_name, directory):
+                path = self._paths.setdefault(path_name, [])
+                path.append(directory)
+
+            # Add paths if they exist.
+            for var, directory in [
+                    ('PATH', self.pkg.prefix.bin),
+                    ('MANPATH', self.pkg.prefix.man),
+                    ('MANPATH', self.pkg.prefix.share_man),
+                    ('LD_LIBRARY_PATH', self.pkg.prefix.lib),
+                    ('LD_LIBRARY_PATH', self.pkg.prefix.lib64)]:
+
+                if os.path.isdir(directory):
+                    add_path(var, directory)
+
+            # short description is just the package + version
+            # TODO: maybe packages can optionally provide it.
+            self.short_description = self.pkg.spec.format("$_ $@")
+
+            # long description is the docstring with reduced whitespace.
+            if self.pkg.__doc__:
+                self.long_description = re.sub(r'\s+', ' ', self.pkg.__doc__)
+
+        return self._paths
+
+
+    def write(self):
+        """Write out a module file for this object."""
+        module_dir = os.path.dirname(self.file_name)
+        if not os.path.exists():
+            mkdirp(module_dir)
+
+        # If there are no paths, no need for a dotkit.
+        if not self.paths:
+            return
+
+        with closing(open(self.file_name)) as f:
+            self._write(f)
+
+
+    def _write(self, stream):
+        """To be implemented by subclasses."""
+        raise NotImplementedError()
+
+
+    @property
+    def file_name(self):
+        """Subclasses should implement this to return the name of the file
+           where this module lives."""
+        return self.pkg.spec.format('$_$@$%@$+$=$#')
+
+
+    def remove(self):
+        mod_file = self.file_name
+        if os.path.exists(mod_file):
+            shutil.rmtree(mod_file, ignore_errors=True)
+
+
+class Dotkit(EnvModule):
+    @property
+    def file_name(self):
+        spec = self.pkg.spec
+        return join_path(dotkit_path, spec.architecture,
+                         spec.format('$_$@$%@$+$#.dk'))
+
+
+    def _write(self, dk_file):
+        # Category
+        if self.category:
+            dk_file.write('#c %s\n' % self.category)
+
+        # Short description
+        if self.short_description:
+            dk_file.write('#d %s\n' % self.short_description)
+
+        # Long description
+        if self.long_description:
+            for line in textwrap.wrap(self.long_description, 72):
+                dk_file.write("#h %s\n" % line)
+
+        # Path alterations
+        for var, dirs in self.paths.items():
+            for directory in dirs:
+                dk_file.write("dk_alter %s %s\n" % (var, directory))
+
+        # Let CMake find this package.
+        dk_file.write("dk_alter CMAKE_PREFIX_PATH %s\n" % pkg.prefix)
+
+
+class TclModule(EnvModule):
+    @property
+    def file_name(self):
+        spec = self.pkg.spec
+        return join_path(tcl_mod_path, spec.architecture,
+                         spec.format('$_$@$%@$+$#'))
+
+
+    def _write(self, m_file):
+        # TODO: cateogry?
+        m_file.write('#%Module1.0\n')
+
+        # Short description
+        if self.short_description:
+            m_file.write('module-whatis \"%s\"\n\n' % self.short_description)
+
+        # Long description
+        if self.long_description:
+            m_file.write('proc ModulesHelp { } {\n')
+            doc = re.sub(r'"', '\"', self.long_description)
+            m_file.write("puts stderr \"%s\"\n" % doc)
+            m_file.write('}\n\n')
+
+        # Path alterations
+        for var, dirs in self.paths.items():
+            for directory in dirs:
+                m_file.write("prepend-path %s \"%s\"\n" % (var, directory))
+
+        m_file.write("prepend-path CMAKE_PREFIX_PATH \"%s\"\n" % pkg.prefix)
diff --git a/share/spack/setup-env.bash b/share/spack/setup-env.sh
similarity index 56%
rename from share/spack/setup-env.bash
rename to share/spack/setup-env.sh
index c23a5acab43..7cadc6f2022 100755
--- a/share/spack/setup-env.bash
+++ b/share/spack/setup-env.sh
@@ -23,16 +23,13 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 
-#
 #
 # This file is part of Spack and sets up the spack environment for
-# bash shells.  This includes dotkit support as well as putting spack
-# in your path.  Source it like this:
+# bash and zsh.  This includes dotkit support, module support, and
+# it also puts spack in your path.  Source it like this:
 #
-#    . /path/to/spack/share/spack/setup-env.bash
+#    . /path/to/spack/share/spack/setup-env.sh
 #
-#
-
 
 ########################################################################
 # This is a wrapper around the spack command that forwards calls to
@@ -59,56 +56,46 @@
 # spack dotfiles.
 ########################################################################
 function spack {
-    _spack_subcommand=$1; shift
-    _spack_spec="$@"
+    _sp_subcommand=$1; shift
+    _sp_spec="$@"
 
     # Filter out use and unuse.  For any other commands, just run the
     # command.
-    case $_spack_subcommand in
-        "use"|"unuse")
+    case $_sp_subcommand in
+        "use"|"unuse"|"load"|"unload")
             # Shift any other args for use off before parsing spec.
-            _spack_use_args=""
+            _sp_module_args=""
             if [[ "$1" =~ ^- ]]; then
-                _spack_use_args="$1"; shift
-                _spack_spec="$@"
+                _sp_module_args="$1"; shift
+                _sp_spec="$@"
             fi
 
-            # Here the user has run use or unuse with a spec.  Find a matching
-            # spec with a dotkit using spack dotkit, then use or unuse the
-            # result.  If spack dotkit comes back with an error, do nothing.
-            if _spack_full_spec=$(command spack dotkit $_spack_spec); then
-                $_spack_subcommand $_spack_use_args $_spack_full_spec
-            fi
-            return
-            ;;
-        "load"|"unload")
-            # Shift any other args for module off before parsing spec.
-            _spack_module_args=""
-            if [[ "$1" =~ ^- ]]; then
-                _spack_module_args="$1"; shift
-                _spack_spec="$@"
-            fi
+            # Translate the parameter into pieces of a command.
+            # _sp_modtype is an arg to spack module find, and
+            # _sp_sh_cmd is the equivalent shell command.
+            case $_sp_subcommand in
+                "use"|"unuse")
+                    _sp_modtype=dotkit
+                    _sp_sh_cmd=$_sp_subcommand
+                    ;;
+                "load"|"unload")
+                    _sp_modtype=tcl
+                    _sp_sh_cmd="module $_sp_subcommand"
+                    ;;
+            esac
 
             # Here the user has run use or unuse with a spec.  Find a matching
-            # spec with a dotkit using spack dotkit, then use or unuse the
-            # result.  If spack dotkit comes back with an error, do nothing.
-            if _spack_full_spec=$(command spack tclmodule $_spack_spec); then
-                $_spack_subcommand $_spack_module_args $_spack_full_spec
+            # spec using 'spack module find', then use the appropriate module
+            # tool's commands to add/remove the result from the environment.
+            # If spack module command comes back with an error, do nothing.
+            if _sp_full_spec=$(command spack module find $_sp_modtype $_sp_spec); then
+                $_sp_sh_cmd $_sp_module_args $_sp_full_spec
             fi
             return
             ;;
         *)
-            command spack $_spack_subcommand "$@"
-            return
-            ;;
+            command spack $_sp_subcommand $_sp_spec
     esac
-
-    # If no args or -h, just run that command as well.
-    if [ -z "$1" -o "$1" = "-h" ]; then
-        command spack $_spack_subcommand -h
-        return
-    fi
-
 }
 
 ########################################################################
@@ -119,31 +106,45 @@ function spack {
 function _spack_pathadd {
     # If no variable name is supplied, just append to PATH
     # otherwise append to that variable.
-    varname=PATH
-    path="$1"
+    _pa_varname=PATH
+    _pa_new_path="$1"
     if [ -n "$2" ]; then
-        varname="$1"
-        path="$2"
+        _pa_varname="$1"
+        _pa_new_path="$2"
     fi
 
     # Do the actual prepending here.
-    eval "oldvalue=\"\$$varname\""
-    if [ -d "$path" ] && [[ ":$oldvalue:" != *":$path:"* ]]; then
-        if [ -n "$oldvalue" ]; then
-            eval "export $varname=\"$path:$oldvalue\""
+    eval "_pa_oldvalue=\$${_pa_varname}"
+
+    if [ -d "$_pa_new_path" ] && [[ ":$_pa_oldvalue:" != *":$_pa_new_path:"* ]]; then
+        if [ -n "$_pa_oldvalue" ]; then
+            eval "export $_pa_varname=\"$_pa_new_path:$_pa_oldvalue\""
         else
-            export $varname="$path"
+            export $_pa_varname="$_pa_new_path"
         fi
     fi
 }
 
+#
+# Figure out where this file is.  Below code needs to be portable to
+# bash and zsh.
+#
+_sp_source_file="${BASH_SOURCE[0]}"  # Bash's location of last sourced file.
+if [ -z "$_sp_source_file" ]; then
+    _sp_source_file="$0:A"           # zsh way to do it
+    if [[ "$_sp_source_file" == *":A" ]]; then
+        # Not zsh either... bail out with plain old $0,
+        # which WILL NOT work if this is sourced indirectly.
+        _sp_source_file="$0"
+    fi
+fi
 
 #
-# Set up dotkit and path in the user environment
+# Set up modules and dotkit search paths in the user environment
 #
-_spack_share_dir="$(dirname ${BASH_SOURCE[0]})"
-_spack_prefix="$(dirname $(dirname $_spack_share_dir))"
+_sp_share_dir="$(dirname $_sp_source_file)"
+_sp_prefix="$(dirname $(dirname $_sp_share_dir))"
 
-_spack_pathadd DK_NODE "$_spack_share_dir/dotkit"
-_spack_pathadd MODULEPATH "$_spack_share_dir/modules"
-_spack_pathadd PATH    "$_spack_prefix/bin"
+_spack_pathadd DK_NODE    "$_sp_share_dir/dotkit"
+_spack_pathadd MODULEPATH "$_sp_share_dir/modules"
+_spack_pathadd PATH       "$_sp_prefix/bin"
diff --git a/share/spack/setup-env.zsh b/share/spack/setup-env.zsh
deleted file mode 100755
index 9aba92818d7..00000000000
--- a/share/spack/setup-env.zsh
+++ /dev/null
@@ -1,122 +0,0 @@
-##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Written by David Beckingsale, david@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
-# the Free Software Foundation) version 2.1 dated 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 General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-
-#
-#
-# This file is part of Spack and sets up the spack environment for zsh shells.
-# This includes dotkit and module support as well as putting spack
-# in your path.  Source it like this:
-#
-#    source /path/to/spack/share/spack/setup-env.zsh
-#
-#
-
-
-########################################################################
-# This is a wrapper around the spack command that forwards calls to
-# 'spack use' and 'spack unuse' to shell functions.  This in turn
-# allows them to be used to invoke dotkit functions.
-#
-# 'spack use' is smarter than just 'use' because it converts its
-# arguments into a unique spack spec that is then passed to dotkit
-# commands.  This allows the user to use packages without knowing all
-# their installation details.
-#
-# e.g., rather than requring a full spec for libelf, the user can type:
-#
-#     spack use libelf
-#
-# This will first find the available libelf dotkits and use a
-# matching one.  If there are two versions of libelf, the user would
-# need to be more specific, e.g.:
-#
-#     spack use libelf@0.8.13
-#
-# This is very similar to how regular spack commands work and it
-# avoids the need to come up with a user-friendly naming scheme for
-# spack dotfiles.
-########################################################################
-function spack {
-    _spack_subcommand=${1}; shift
-    _spack_spec="$@"
-
-    # Filter out use and unuse.  For any other commands, just run the
-    # command.
-    case ${_spack_subcommand} in
-        "use"|"unuse")
-            # Shift any other args for use off before parsing spec.
-            _spack_use_args=""
-            if [[ "$1" =~ ^- ]]; then
-                _spack_use_args="$1"; shift
-                _spack_spec="$@"
-            fi
-
-            # Here the user has run use or unuse with a spec.  Find a matching
-            # spec with a dotkit using spack dotkit, then use or unuse the
-            # result.  If spack dotkit comes back with an error, do nothing.
-            if _spack_full_spec=$(command spack dotkit $_spack_spec); then
-                $_spack_subcommand $_spack_use_args $_spack_full_spec
-            fi
-            return
-            ;;
-        "load"|"unload")
-            # Shift any other args for module off before parsing spec.
-            _spack_module_args=""
-            if [[ "$1" =~ ^- ]]; then
-                _spack_module_args="$1"; shift
-                _spack_spec="$@"
-            fi
-
-            # Here the user has run use or unuse with a spec.  Find a matching
-            # spec with a dotkit using spack dotkit, then use or unuse the
-            # result.  If spack dotkit comes back with an error, do nothing.
-            if _spack_full_spec=$(command spack tclmodule ${_spack_spec}); then
-                module ${_spack_subcommand} ${_spack_module_args} ${_spack_full_spec}
-            fi
-            return
-            ;;
-        *)
-            command spack $_spack_subcommand "$@"
-            return
-            ;;
-    esac
-
-    # If no args or -h, just run that command as well.
-    if [ -z "$1" -o "$1" = "-h" ]; then
-        command spack $_spack_subcommand -h
-        return
-    fi
-
-}
-
-#
-# Set up dotkit and path in the user environment
-#
-_spack_share_dir="$(dirname $0:A)"
-_spack_prefix="$(dirname $(dirname ${_spack_share_dir}))"
-
-export DK_NODE="$_spack_share_dir/dotkit:$DK_NODE"
-export MODULEPATH="$_spack_share_dir/modules:$MODULEPATH"
-export PATH="$_spack_prefix/bin:$PATH"

From 776560f8ce9f464548cc116117c6a58b686448ff Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 16 Aug 2014 14:58:15 -0700
Subject: [PATCH 53/71] Add csh/tcsh support for modules

- csh scripting is a GIANT pain in the ass
- hopefully the thin script layer doesn't get much more complex.
---
 lib/spack/spack/modules.py        |  1 +
 share/spack/csh/spack.csh         | 71 +++++++++++++++++++++++++++++++
 share/spack/csh/spack_pathadd.csh | 23 ++++++++++
 share/spack/setup-env.csh         | 46 ++++++++++++++++++++
 4 files changed, 141 insertions(+)
 create mode 100644 share/spack/csh/spack.csh
 create mode 100644 share/spack/csh/spack_pathadd.csh
 create mode 100755 share/spack/setup-env.csh

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 8ac7e470cb5..0f8c4177932 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -71,6 +71,7 @@ def print_help():
             "    . %s/setup-env.sh" % spack.share_path,
             "",
             "For csh and tcsh:",
+            "    setenv SPACK_ROOT %s"    % spack.prefix,
             "    source %s/setup-env.csh" % spack.share_path,
             "")
 
diff --git a/share/spack/csh/spack.csh b/share/spack/csh/spack.csh
new file mode 100644
index 00000000000..2f6b96f4ebd
--- /dev/null
+++ b/share/spack/csh/spack.csh
@@ -0,0 +1,71 @@
+########################################################################
+# This is a wrapper around the spack command that forwards calls to
+# 'spack use' and 'spack unuse' to shell functions.  This in turn
+# allows them to be used to invoke dotkit functions.
+#
+# 'spack use' is smarter than just 'use' because it converts its
+# arguments into a unique spack spec that is then passed to dotkit
+# commands.  This allows the user to use packages without knowing all
+# their installation details.
+#
+# e.g., rather than requring a full spec for libelf, the user can type:
+#
+#     spack use libelf
+#
+# This will first find the available libelf dotkits and use a
+# matching one.  If there are two versions of libelf, the user would
+# need to be more specific, e.g.:
+#
+#     spack use libelf@0.8.13
+#
+# This is very similar to how regular spack commands work and it
+# avoids the need to come up with a user-friendly naming scheme for
+# spack dotfiles.
+########################################################################
+# Set up args -- we want a subcommand and a spec.
+set _sp_subcommand="";
+set _sp_spec="";
+[ $#_sp_args -gt 0 ] && set _sp_subcommand = ($_sp_args[1]);
+[ $#_sp_args -gt 1 ] && set _sp_spec = ($_sp_args[2-]);
+
+# Figure out what type of module we're running here.
+set _sp_modtype = "";
+switch ($_sp_subcommand)
+case use:
+case unuse:
+case load:
+case unload:
+    set _sp_module_args=""""
+    if ( "$_sp_spec" =~ "-*" ) then
+        set _sp_module_args = $_sp_spec[1]
+        shift _sp_spec
+        set _sp_spec = ($_sp_spec)
+    endif
+    # Translate the parameter into pieces of a command.
+    # _sp_modtype is an arg to spack module find, and
+    # _sp_sh_cmd is the equivalent shell command.
+    switch ($_sp_subcommand)
+        case use:
+        case unuse:
+            set _sp_modtype = dotkit
+            set _sp_sh_cmd = $_sp_subcommand
+            breaksw
+        case load:
+        case unload:
+            set _sp_modtype = tcl
+            set _sp_sh_cmd = ( module $_sp_subcommand )
+            breaksw
+    endsw
+
+    # Here the user has run use or unuse with a spec.  Find a matching
+    # spec using 'spack module find', then use the appropriate module
+    # tool's commands to add/remove the result from the environment.
+    # If spack module command comes back with an error, do nothing.
+    if { set _sp_full_spec = `command spack module find $_sp_modtype $_sp_spec` } then
+        echo $_sp_sh_cmd $_sp_module_args $_sp_full_spec
+    endif
+default:
+    command spack $_sp_args
+endsw
+
+unset _sp_args _sp_full_spec _sp_modtype _sp_module_args _sp_sh_cmd _sp_spec _sp_subcommand
diff --git a/share/spack/csh/spack_pathadd.csh b/share/spack/csh/spack_pathadd.csh
new file mode 100644
index 00000000000..1e0800c5f3f
--- /dev/null
+++ b/share/spack/csh/spack_pathadd.csh
@@ -0,0 +1,23 @@
+########################################################################
+# Prepends directories to path, if they exist.
+#      pathadd /path/to/dir            # add to PATH
+# or   pathadd OTHERPATH /path/to/dir  # add to OTHERPATH
+########################################################################
+# If no variable name is supplied, just append to PATH
+# otherwise append to that variable.
+set _pa_varname = PATH;
+set _pa_new_path = $_pa_args[1];
+[ $#_pa_args -gt 1 ] && set _pa_varname = $_pa_args[1] && set _pa_new_path = $_pa_args[2];
+
+# Check whether the variable is set yet.
+set _pa_old_value = ""
+eval set _pa_set = '$?'$_pa_varname
+[ $_pa_set -eq 1 ] && eval set _pa_old_value='$'$_pa_varname;
+
+# Do the actual prepending here, if it is a dir and not already in the path
+if ( -d $_pa_new_path && \:$_pa_old_value\: !~ *\:$_pa_new_path\:* ) then
+    [ -n "$_pa_old_value" ] && setenv $_pa_varname $_pa_new_path\:$_pa_old_value
+    [ -z "$_pa_old_value" ] && setenv $_pa_varname $_pa_new_path
+endif
+
+unset _pa_args _pa_new_path _pa_old_value _pa_set _pa_varname
diff --git a/share/spack/setup-env.csh b/share/spack/setup-env.csh
new file mode 100755
index 00000000000..e3243e40b27
--- /dev/null
+++ b/share/spack/setup-env.csh
@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+#
+# This file is part of Spack and sets up the spack environment for
+# csh and tcsh.  This includes dotkit support, module support, and
+# it also puts spack in your path.  Source it like this:
+#
+#    setenv SPACK_ROOT /path/to/spack
+#    source $SPACK_ROOT/share/spack/setup-env.csh
+#
+if ($?SPACK_ROOT) then
+    set _spack_source_file = $SPACK_ROOT/share/spack/setup-env.csh
+    set _spack_share_dir   = $SPACK_ROOT/share/spack
+
+    # Command aliases point at separate source files
+    alias spack          'set _sp_args = (\!*); source $_spack_share_dir/csh/spack.csh'
+    alias _spack_pathadd 'set _pa_args = (\!*) && source $_spack_share_dir/csh/spack_pathadd.csh'
+
+    # Set up modules and dotkit search paths in the user environment
+    _spack_pathadd DK_NODE    "$_spack_share_dir/dotkit"
+    _spack_pathadd MODULEPATH "$_spack_share_dir/modules"
+    _spack_pathadd PATH       "$SPACK_ROOT/bin"
+endif

From 22bec329c1824ecd3271fffcef9ff793363ba93d Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 16 Aug 2014 22:22:34 -0700
Subject: [PATCH 54/71] Bugfixes, more consolidation of modules code.

- specific module classes use __metaclass__ to register themselves.
- bugfixes in module writing.
---
 .gitignore                    |  1 +
 lib/spack/spack/cmd/module.py | 25 +++++++++++++------------
 lib/spack/spack/modules.py    | 35 ++++++++++++++++++++++++++---------
 lib/spack/spack/packages.py   | 10 ++++++++++
 4 files changed, 50 insertions(+), 21 deletions(-)

diff --git a/.gitignore b/.gitignore
index d6e0d3e60c2..828fb04e7d0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@
 .idea
 /etc/spackconfig
 /share/spack/dotkit
+/share/spack/modules
diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py
index ead3b9abac8..af5a68923b2 100644
--- a/lib/spack/spack/cmd/module.py
+++ b/lib/spack/spack/cmd/module.py
@@ -32,18 +32,13 @@
 from llnl.util.filesystem import mkdirp
 
 import spack.cmd
-import spack.modules
+from spack.modules import module_types
 from spack.util.string import *
 
 from spack.spec import Spec
 
 description ="Manipulate modules and dotkits."
 
-module_types = {
-    'dotkit' : spack.modules.Dotkit,
-    'tcl'    : spack.modules.TclModule
-}
-
 
 def setup_parser(subparser):
     sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='module_command')
@@ -87,13 +82,19 @@ def module_find(mtype, spec_array):
 
 
 def module_refresh():
-    shutil.rmtree(spack.dotkit_path, ignore_errors=False)
-    mkdirp(spack.dotkit_path)
+    """Regenerate all module files for installed packages known to
+       spack (some packages may no longer exist)."""
+    specs = [s for s in spack.db.installed_known_package_specs()]
+
+    for name, cls in module_types.items():
+        tty.msg("Regenerating %s module files." % name)
+        if os.path.isdir(cls.path):
+            shutil.rmtree(cls.path, ignore_errors=False)
+        mkdirp(cls.path)
+        for spec in specs:
+            tty.debug("   Writing file for %s." % spec)
+            cls(spec.package).write()
 
-    specs = spack.db.installed_package_specs()
-    for spec in specs:
-        for mt in module_types:
-            mt(spec.package).write()
 
 
 def module(parser, args):
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 0f8c4177932..596308f801d 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -56,8 +56,10 @@
 
 import spack
 
-dotkit_path  = join_path(spack.share_path, "dotkit")
-tcl_mod_path = join_path(spack.share_path, "modules")
+"""Registry of all types of modules.  Entries created by EnvModule's
+   metaclass."""
+module_types = {}
+
 
 def print_help():
     """For use by commands to tell user how to activate shell support."""
@@ -77,6 +79,15 @@ def print_help():
 
 
 class EnvModule(object):
+    name = 'env_module'
+
+    class __metaclass__(type):
+        def __init__(cls, name, bases, dict):
+            type.__init__(cls, name, bases, dict)
+            if cls.name != 'env_module':
+                module_types[cls.name] = cls
+
+
     def __init__(self, pkg=None):
         # category in the modules system
         # TODO: come up with smarter category names.
@@ -97,7 +108,7 @@ def paths(self):
         if self._paths is None:
             self._paths = {}
 
-            def add_path(self, path_name, directory):
+            def add_path(path_name, directory):
                 path = self._paths.setdefault(path_name, [])
                 path.append(directory)
 
@@ -126,14 +137,14 @@ def add_path(self, path_name, directory):
     def write(self):
         """Write out a module file for this object."""
         module_dir = os.path.dirname(self.file_name)
-        if not os.path.exists():
+        if not os.path.exists(module_dir):
             mkdirp(module_dir)
 
         # If there are no paths, no need for a dotkit.
         if not self.paths:
             return
 
-        with closing(open(self.file_name)) as f:
+        with closing(open(self.file_name, 'w')) as f:
             self._write(f)
 
 
@@ -156,10 +167,13 @@ def remove(self):
 
 
 class Dotkit(EnvModule):
+    name = 'dotkit'
+    path = join_path(spack.share_path, "dotkit")
+
     @property
     def file_name(self):
         spec = self.pkg.spec
-        return join_path(dotkit_path, spec.architecture,
+        return join_path(Dotkit.path, spec.architecture,
                          spec.format('$_$@$%@$+$#.dk'))
 
 
@@ -183,14 +197,17 @@ def _write(self, dk_file):
                 dk_file.write("dk_alter %s %s\n" % (var, directory))
 
         # Let CMake find this package.
-        dk_file.write("dk_alter CMAKE_PREFIX_PATH %s\n" % pkg.prefix)
+        dk_file.write("dk_alter CMAKE_PREFIX_PATH %s\n" % self.pkg.prefix)
 
 
 class TclModule(EnvModule):
+    name = 'tcl'
+    path = join_path(spack.share_path, "modules")
+
     @property
     def file_name(self):
         spec = self.pkg.spec
-        return join_path(tcl_mod_path, spec.architecture,
+        return join_path(TclModule.path, spec.architecture,
                          spec.format('$_$@$%@$+$#'))
 
 
@@ -214,4 +231,4 @@ def _write(self, m_file):
             for directory in dirs:
                 m_file.write("prepend-path %s \"%s\"\n" % (var, directory))
 
-        m_file.write("prepend-path CMAKE_PREFIX_PATH \"%s\"\n" % pkg.prefix)
+        m_file.write("prepend-path CMAKE_PREFIX_PATH \"%s\"\n" % self.pkg.prefix)
diff --git a/lib/spack/spack/packages.py b/lib/spack/spack/packages.py
index 00834c95d54..f9840a5c057 100644
--- a/lib/spack/spack/packages.py
+++ b/lib/spack/spack/packages.py
@@ -118,6 +118,16 @@ def installed_package_specs(self):
         return spack.install_layout.all_specs()
 
 
+    def installed_known_package_specs(self):
+        """Read installed package names straight from the install
+           directory layout, but return only specs for which the
+           package is known to this version of spack.
+        """
+        for spec in spack.install_layout.all_specs():
+            if self.exists(spec.name):
+                yield spec
+
+
     @memoized
     def all_package_names(self):
         """Generator function for all packages.  This looks for

From b601fd08caf21b5fc11e6998a5ebd20a04ac57ad Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 17 Aug 2014 01:41:32 -0700
Subject: [PATCH 55/71] Bugfixes for csh environment modules.

---
 lib/spack/spack/cmd/module.py | 15 ++++++++-----
 lib/spack/spack/modules.py    | 27 ++++++++++++++++------
 share/spack/csh/spack.csh     | 42 ++++++++++++++++++++++++++---------
 share/spack/setup-env.csh     |  5 +++--
 share/spack/setup-env.sh      | 22 ++++++++++++++----
 5 files changed, 81 insertions(+), 30 deletions(-)

diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py
index af5a68923b2..4f6de18532e 100644
--- a/lib/spack/spack/cmd/module.py
+++ b/lib/spack/spack/cmd/module.py
@@ -52,14 +52,16 @@ def setup_parser(subparser):
 
 
 def module_find(mtype, spec_array):
+    """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.
+    """
     specs = spack.cmd.parse_specs(spec_array)
     if len(specs) > 1:
         tty.die("You can only pass one spec.")
     spec = specs[0]
 
-    if not spack.db.exists(spec.name):
-        tty.die("No such package: %s" % spec.name)
-
     if mtype not in module_types:
         tty.die("Invalid module type: '%s'.  Options are " + comma_and(module_types))
 
@@ -74,11 +76,12 @@ def module_find(mtype, spec_array):
         sys.exit(1)
 
     mt = module_types[mtype]
-    mod = mt(spec.package)
+    mod = mt(specs[0].package)
     if not os.path.isfile(mod.file_name):
-        tty.die("No dotkit is installed for package %s." % spec)
+        tty.error( mod.file_name)
+        tty.die("No %s module is installed for package %s." % (mtype, spec))
 
-    print mod.file_name
+    print mod.use_name
 
 
 def module_refresh():
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 596308f801d..3f56208f5b0 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -157,7 +157,14 @@ def _write(self, stream):
     def file_name(self):
         """Subclasses should implement this to return the name of the file
            where this module lives."""
-        return self.pkg.spec.format('$_$@$%@$+$=$#')
+        raise NotImplementedError()
+
+
+    @property
+    def use_name(self):
+        """Subclasses should implement this to return the name the
+           module command uses to refer to the package."""
+        raise NotImplementedError()
 
 
     def remove(self):
@@ -172,9 +179,12 @@ class Dotkit(EnvModule):
 
     @property
     def file_name(self):
-        spec = self.pkg.spec
-        return join_path(Dotkit.path, spec.architecture,
-                         spec.format('$_$@$%@$+$#.dk'))
+        return join_path(Dotkit.path, self.pkg.spec.architecture,
+                         self.pkg.spec.format('$_$@$%@$+$#.dk'))
+
+    @property
+    def use_name(self):
+        return self.pkg.spec.format('$_$@$%@$+$#')
 
 
     def _write(self, dk_file):
@@ -206,9 +216,12 @@ class TclModule(EnvModule):
 
     @property
     def file_name(self):
-        spec = self.pkg.spec
-        return join_path(TclModule.path, spec.architecture,
-                         spec.format('$_$@$%@$+$#'))
+        return join_path(TclModule.path, self.pkg.spec.architecture, self.use_name)
+
+
+    @property
+    def use_name(self):
+        return self.pkg.spec.format('$_$@$%@$+$#')
 
 
     def _write(self, m_file):
diff --git a/share/spack/csh/spack.csh b/share/spack/csh/spack.csh
index 2f6b96f4ebd..169e9878bfc 100644
--- a/share/spack/csh/spack.csh
+++ b/share/spack/csh/spack.csh
@@ -22,14 +22,28 @@
 # avoids the need to come up with a user-friendly naming scheme for
 # spack dotfiles.
 ########################################################################
+# accumulate initial flags for main spack command
+set _sp_flags = ""
+while ( $#_sp_args > 0 )
+    if ( "$_sp_args[1]" !~ "-*" ) break
+    set _sp_flags = "$_sp_flags $_sp_args[1]"
+    shift _sp_args
+end
+
+# h and V flags don't require further output parsing.
+if ( "$_sp_flags" =~ *h* || "$_sp_flags" =~ *V* ) then
+    \spack $_sp_flags $_sp_args
+    goto _sp_end
+endif
+
 # Set up args -- we want a subcommand and a spec.
-set _sp_subcommand="";
-set _sp_spec="";
-[ $#_sp_args -gt 0 ] && set _sp_subcommand = ($_sp_args[1]);
-[ $#_sp_args -gt 1 ] && set _sp_spec = ($_sp_args[2-]);
+set _sp_subcommand=""
+set _sp_spec=""
+[ $#_sp_args -gt 0 ] && set _sp_subcommand = ($_sp_args[1])
+[ $#_sp_args -gt 1 ] && set _sp_spec = ($_sp_args[2-])
 
 # Figure out what type of module we're running here.
-set _sp_modtype = "";
+set _sp_modtype = ""
 switch ($_sp_subcommand)
 case use:
 case unuse:
@@ -48,12 +62,12 @@ case unload:
         case use:
         case unuse:
             set _sp_modtype = dotkit
-            set _sp_sh_cmd = $_sp_subcommand
+            set _sp_sh_cmd = ( "`alias $_sp_subcommand'" )
             breaksw
         case load:
         case unload:
             set _sp_modtype = tcl
-            set _sp_sh_cmd = ( module $_sp_subcommand )
+            set _sp_sh_cmd = ( "`alias module`" $_sp_subcommand )
             breaksw
     endsw
 
@@ -61,11 +75,17 @@ case unload:
     # spec using 'spack module find', then use the appropriate module
     # tool's commands to add/remove the result from the environment.
     # If spack module command comes back with an error, do nothing.
-    if { set _sp_full_spec = `command spack module find $_sp_modtype $_sp_spec` } then
-        echo $_sp_sh_cmd $_sp_module_args $_sp_full_spec
+    set _sp_full_spec = ""
+    if { set _sp_full_spec = `\spack module find $_sp_modtype $_sp_spec` } then
+         $_sp_sh_cmd $_sp_module_args $_sp_full_spec
     endif
+    breaksw
+
 default:
-    command spack $_sp_args
+    \spack $_sp_args
+    breaksw
 endsw
 
-unset _sp_args _sp_full_spec _sp_modtype _sp_module_args _sp_sh_cmd _sp_spec _sp_subcommand
+_sp_end:
+unset _sp_args _sp_full_spec _sp_modtype _sp_module_args
+unset _sp_sh_cmd _sp_spec _sp_subcommand _sp_flags
diff --git a/share/spack/setup-env.csh b/share/spack/setup-env.csh
index e3243e40b27..cc12eae82f5 100755
--- a/share/spack/setup-env.csh
+++ b/share/spack/setup-env.csh
@@ -40,7 +40,8 @@ if ($?SPACK_ROOT) then
     alias _spack_pathadd 'set _pa_args = (\!*) && source $_spack_share_dir/csh/spack_pathadd.csh'
 
     # Set up modules and dotkit search paths in the user environment
-    _spack_pathadd DK_NODE    "$_spack_share_dir/dotkit"
-    _spack_pathadd MODULEPATH "$_spack_share_dir/modules"
+    # TODO: fix SYS_TYPE to something non-LLNL-specific
+    _spack_pathadd DK_NODE    "$_spack_share_dir/dotkit/$SYS_TYPE"
+    _spack_pathadd MODULEPATH "$_spack_share_dir/modules/$SYS_TYPE"
     _spack_pathadd PATH       "$SPACK_ROOT/bin"
 endif
diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh
index 7cadc6f2022..0142e048172 100755
--- a/share/spack/setup-env.sh
+++ b/share/spack/setup-env.sh
@@ -56,6 +56,19 @@
 # spack dotfiles.
 ########################################################################
 function spack {
+    # accumulate initial flags for main spack command
+    _sp_flags=""
+    while [[ "$1" =~ ^- ]]; do
+        _sp_flags="$_sp_flags $1"
+        shift
+    done
+
+    # h and V flags don't require further output parsing.
+    if [[ "$_sp_flags" =~ *h* || "$_sp_flags" =~ *V* ]]; then
+        command spack $_sp_flags "$@"
+        return
+    fi
+
     _sp_subcommand=$1; shift
     _sp_spec="$@"
 
@@ -88,13 +101,13 @@ function spack {
             # spec using 'spack module find', then use the appropriate module
             # tool's commands to add/remove the result from the environment.
             # If spack module command comes back with an error, do nothing.
-            if _sp_full_spec=$(command spack module find $_sp_modtype $_sp_spec); then
+            if _sp_full_spec=$(command spack $_sp_flags module find $_sp_modtype $_sp_spec); then
                 $_sp_sh_cmd $_sp_module_args $_sp_full_spec
             fi
             return
             ;;
         *)
-            command spack $_sp_subcommand $_sp_spec
+            command spack $_sp_flags $_sp_subcommand $_sp_spec
     esac
 }
 
@@ -145,6 +158,7 @@ fi
 _sp_share_dir="$(dirname $_sp_source_file)"
 _sp_prefix="$(dirname $(dirname $_sp_share_dir))"
 
-_spack_pathadd DK_NODE    "$_sp_share_dir/dotkit"
-_spack_pathadd MODULEPATH "$_sp_share_dir/modules"
+# TODO: fix SYS_TYPE to something non-LLNL-specific
+_spack_pathadd DK_NODE    "$_sp_share_dir/dotkit/$SYS_TYPE"
+_spack_pathadd MODULEPATH "$_sp_share_dir/modules/$SYS_TYPE"
 _spack_pathadd PATH       "$_sp_prefix/bin"

From 5a9ef130ea51f02a486b18f7173b980f3a539440 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 20 Aug 2014 11:43:03 -0700
Subject: [PATCH 56/71] Make EnvModule class use spec instead of package, fix
 using module of non-present package.

- Using the spec doesn't require the package to be there.
- Restore ability to use non-present packages (which was broken)
---
 lib/spack/spack/cmd/module.py   | 13 ++++++-------
 lib/spack/spack/hooks/dotkit.py |  4 ++--
 lib/spack/spack/modules.py      | 34 ++++++++++++++++-----------------
 lib/spack/spack/util/string.py  |  4 +++-
 4 files changed, 28 insertions(+), 27 deletions(-)

diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py
index f23f3d2f9f2..34f0855a50b 100644
--- a/lib/spack/spack/cmd/module.py
+++ b/lib/spack/spack/cmd/module.py
@@ -57,14 +57,14 @@ def module_find(mtype, spec_array):
        of type <mtype> there, and print out the name that the user
        should type to use that package's module.
     """
+    if mtype not in module_types:
+        tty.die("Invalid module type: '%s'.  Options are %s." % (mtype, comma_or(module_types)))
+
     specs = spack.cmd.parse_specs(spec_array)
     if len(specs) > 1:
         tty.die("You can only pass one spec.")
     spec = specs[0]
 
-    if mtype not in module_types:
-        tty.die("Invalid module type: '%s'.  Options are " + comma_and(module_types))
-
     specs = [s for s in spack.db.installed_package_specs() if s.satisfies(spec)]
     if len(specs) == 0:
         tty.die("No installed packages match spec %s" % spec)
@@ -76,10 +76,9 @@ def module_find(mtype, spec_array):
         sys.exit(1)
 
     mt = module_types[mtype]
-    mod = mt(specs[0].package)
+    mod = mt(specs[0])
     if not os.path.isfile(mod.file_name):
-        tty.error( mod.file_name)
-        tty.die("No %s module is installed for package %s." % (mtype, spec))
+        tty.die("No %s module is installed for %s." % (mtype, spec))
 
     print mod.use_name
 
@@ -96,7 +95,7 @@ def module_refresh():
         mkdirp(cls.path)
         for spec in specs:
             tty.debug("   Writing file for %s." % spec)
-            cls(spec.package).write()
+            cls(spec).write()
 
 
 
diff --git a/lib/spack/spack/hooks/dotkit.py b/lib/spack/spack/hooks/dotkit.py
index 0f46f6a2fcf..4e748ff80a4 100644
--- a/lib/spack/spack/hooks/dotkit.py
+++ b/lib/spack/spack/hooks/dotkit.py
@@ -26,10 +26,10 @@
 
 
 def post_install(pkg):
-    dk = spack.modules.Dotkit(pkg)
+    dk = spack.modules.Dotkit(pkg.spec)
     dk.write()
 
 
 def post_uninstall(pkg):
-    dk = spack.modules.Dotkit(pkg)
+    dk = spack.modules.Dotkit(pkg.spec)
     dk.remove()
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 3f56208f5b0..5d2105e37c0 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -88,7 +88,7 @@ def __init__(cls, name, bases, dict):
                 module_types[cls.name] = cls
 
 
-    def __init__(self, pkg=None):
+    def __init__(self, spec=None):
         # category in the modules system
         # TODO: come up with smarter category names.
         self.category = "spack"
@@ -100,7 +100,7 @@ def __init__(self, pkg=None):
         # dict pathname -> list of directories to be prepended to in
         # the module file.
         self._paths = None
-        self.pkg = pkg
+        self.spec = spec
 
 
     @property
@@ -114,22 +114,22 @@ def add_path(path_name, directory):
 
             # Add paths if they exist.
             for var, directory in [
-                    ('PATH', self.pkg.prefix.bin),
-                    ('MANPATH', self.pkg.prefix.man),
-                    ('MANPATH', self.pkg.prefix.share_man),
-                    ('LD_LIBRARY_PATH', self.pkg.prefix.lib),
-                    ('LD_LIBRARY_PATH', self.pkg.prefix.lib64)]:
+                    ('PATH', self.spec.prefix.bin),
+                    ('MANPATH', self.spec.prefix.man),
+                    ('MANPATH', self.spec.prefix.share_man),
+                    ('LD_LIBRARY_PATH', self.spec.prefix.lib),
+                    ('LD_LIBRARY_PATH', self.spec.prefix.lib64)]:
 
                 if os.path.isdir(directory):
                     add_path(var, directory)
 
             # short description is just the package + version
             # TODO: maybe packages can optionally provide it.
-            self.short_description = self.pkg.spec.format("$_ $@")
+            self.short_description = self.spec.format("$_ $@")
 
             # long description is the docstring with reduced whitespace.
-            if self.pkg.__doc__:
-                self.long_description = re.sub(r'\s+', ' ', self.pkg.__doc__)
+            if self.spec.package.__doc__:
+                self.long_description = re.sub(r'\s+', ' ', self.spec.package.__doc__)
 
         return self._paths
 
@@ -179,12 +179,12 @@ class Dotkit(EnvModule):
 
     @property
     def file_name(self):
-        return join_path(Dotkit.path, self.pkg.spec.architecture,
-                         self.pkg.spec.format('$_$@$%@$+$#.dk'))
+        return join_path(Dotkit.path, self.spec.architecture,
+                         self.spec.format('$_$@$%@$+$#.dk'))
 
     @property
     def use_name(self):
-        return self.pkg.spec.format('$_$@$%@$+$#')
+        return self.spec.format('$_$@$%@$+$#')
 
 
     def _write(self, dk_file):
@@ -207,7 +207,7 @@ def _write(self, dk_file):
                 dk_file.write("dk_alter %s %s\n" % (var, directory))
 
         # Let CMake find this package.
-        dk_file.write("dk_alter CMAKE_PREFIX_PATH %s\n" % self.pkg.prefix)
+        dk_file.write("dk_alter CMAKE_PREFIX_PATH %s\n" % self.spec.prefix)
 
 
 class TclModule(EnvModule):
@@ -216,12 +216,12 @@ class TclModule(EnvModule):
 
     @property
     def file_name(self):
-        return join_path(TclModule.path, self.pkg.spec.architecture, self.use_name)
+        return join_path(TclModule.path, self.spec.architecture, self.use_name)
 
 
     @property
     def use_name(self):
-        return self.pkg.spec.format('$_$@$%@$+$#')
+        return self.spec.format('$_$@$%@$+$#')
 
 
     def _write(self, m_file):
@@ -244,4 +244,4 @@ def _write(self, m_file):
             for directory in dirs:
                 m_file.write("prepend-path %s \"%s\"\n" % (var, directory))
 
-        m_file.write("prepend-path CMAKE_PREFIX_PATH \"%s\"\n" % self.pkg.prefix)
+        m_file.write("prepend-path CMAKE_PREFIX_PATH \"%s\"\n" % self.spec.prefix)
diff --git a/lib/spack/spack/util/string.py b/lib/spack/spack/util/string.py
index e7a9a6862e8..234163bf52c 100644
--- a/lib/spack/spack/util/string.py
+++ b/lib/spack/spack/util/string.py
@@ -33,7 +33,9 @@ def comma_list(sequence, article=''):
         return sequence[0]
     else:
         out =  ', '.join(str(s) for s in sequence[:-1])
-        out += ', '
+        if len(sequence) != 2:
+            out += ','   # oxford comma
+        out += ' '
         if article:
             out += article + ' '
         out += str(sequence[-1])

From e301d623329d3f484316643c6a50dc3df4806dab Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 20 Aug 2014 11:46:59 -0700
Subject: [PATCH 57/71] Remove development TAU version from package.

---
 var/spack/packages/tau/package.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/var/spack/packages/tau/package.py b/var/spack/packages/tau/package.py
index caafe4e2c92..048fac80aa5 100644
--- a/var/spack/packages/tau/package.py
+++ b/var/spack/packages/tau/package.py
@@ -10,9 +10,7 @@ class Tau(Package):
     homepage = "http://www.cs.uoregon.edu/research/tau"
     url      = "http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/tau-2.23.1.tar.gz"
 
-    version('2.23.1',        '6593b47ae1e7a838e632652f0426fe72')
-    version('2.23.2-perfdb', '4048f693eee246d48eb2619c0f05999e',
-            url='http://www.nic.uoregon.edu/~khuck/tau2-latest.tar.gz')
+    version('2.23.1', '6593b47ae1e7a838e632652f0426fe72')
 
     def install(self, spec, prefix):
         # TAU isn't happy with directories that have '@' in the path.  Sigh.

From d87a6525823e0d75b9f6b71fb265ebffb9c060a4 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Fri, 22 Aug 2014 11:00:19 -0700
Subject: [PATCH 58/71] Add spack cd and spack location commands.

- Better shell support for cd'ing into directories
- Fix some csh weirdness with nested aliases.
---
 lib/spack/spack/cmd/cd.py                     | 38 ++++++++
 lib/spack/spack/cmd/location.py               | 93 +++++++++++++++++++
 lib/spack/spack/cmd/mirror.py                 |  2 +-
 lib/spack/spack/cmd/stage.py                  | 30 +-----
 lib/spack/spack/modules.py                    |  6 +-
 .../csh/{spack_pathadd.csh => pathadd.csh}    |  0
 share/spack/csh/spack.csh                     | 50 +++++-----
 share/spack/setup-env.csh                     |  2 +-
 share/spack/setup-env.sh                      | 38 ++++----
 9 files changed, 186 insertions(+), 73 deletions(-)
 create mode 100644 lib/spack/spack/cmd/cd.py
 create mode 100644 lib/spack/spack/cmd/location.py
 rename share/spack/csh/{spack_pathadd.csh => pathadd.csh} (100%)

diff --git a/lib/spack/spack/cmd/cd.py b/lib/spack/spack/cmd/cd.py
new file mode 100644
index 00000000000..24d56db7d0b
--- /dev/null
+++ b/lib/spack/spack/cmd/cd.py
@@ -0,0 +1,38 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 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 spack.cmd.location
+import spack.modules
+
+description="cd to spack directories in the shell."
+
+def setup_parser(subparser):
+    """This is for decoration -- spack cd is used through spack's
+       shell support.  This allows spack cd to print a descriptive
+       help message when called with -h."""
+    spack.cmd.location.setup_parser(subparser)
+
+
+def cd(parser, args):
+    spack.modules.print_help()
diff --git a/lib/spack/spack/cmd/location.py b/lib/spack/spack/cmd/location.py
new file mode 100644
index 00000000000..074d984ee60
--- /dev/null
+++ b/lib/spack/spack/cmd/location.py
@@ -0,0 +1,93 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 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 os
+from external import argparse
+
+import llnl.util.tty as tty
+from llnl.util.filesystem import join_path
+
+import spack
+import spack.cmd
+
+description="Print out locations of various diectories used by Spack"
+
+def setup_parser(subparser):
+    global directories
+    directories = subparser.add_mutually_exclusive_group()
+
+    directories.add_argument(
+        '-m', '--module-dir', action='store_true', help="Spack python module directory.")
+    directories.add_argument(
+        '-r', '--spack-root', action='store_true', help="Spack installation root.")
+
+    directories.add_argument(
+        '-i', '--install-dir', action='store_true',
+        help="Install prefix for spec (spec need not be installed).")
+    directories.add_argument(
+        '-p', '--package-dir', action='store_true',
+        help="Directory enclosing a spec's package.py file.")
+    directories.add_argument(
+        '-s', '--stage-dir', action='store_true', help="Stage directory for a spec.")
+    directories.add_argument(
+        '-b', '--build-dir', action='store_true',
+        help="Expanded archive directory for a spec (requires it to be staged first).")
+
+    subparser.add_argument(
+        'spec', nargs=argparse.REMAINDER, help="spec of package to fetch directory for.")
+
+
+def location(parser, args):
+    if args.module_dir:
+        print spack.module_path
+
+    elif args.spack_root:
+        print spack.prefix
+
+    else:
+        specs = spack.cmd.parse_specs(args.spec, concretize=True)
+        if not specs:
+            tty.die("You must supply a spec.")
+        if len(specs) != 1:
+            tty.die("Too many specs.  Need only one.")
+        spec = specs[0]
+
+        if args.install_dir:
+            print spec.prefix
+
+        elif args.package_dir:
+            print join_path(spack.db.root, spec.name)
+
+        else:
+            pkg = spack.db.get(spec)
+
+            if args.stage_dir:
+                print pkg.stage.path
+
+            else:  #  args.build_dir is the default.
+                if not os.listdir(pkg.stage.path):
+                    tty.die("Build directory does not exist yet. Run this to create it:",
+                            "spack stage " + " ".join(args.spec))
+                print pkg.stage.expanded_archive_path
+
diff --git a/lib/spack/spack/cmd/mirror.py b/lib/spack/spack/cmd/mirror.py
index a039e3383a3..b42b3290858 100644
--- a/lib/spack/spack/cmd/mirror.py
+++ b/lib/spack/spack/cmd/mirror.py
@@ -41,7 +41,7 @@
 from spack.util.compression import extension
 
 
-description = "Manage spack mirrors."
+description = "Manage mirrors."
 
 def setup_parser(subparser):
     subparser.add_argument(
diff --git a/lib/spack/spack/cmd/stage.py b/lib/spack/spack/cmd/stage.py
index 5df0ffc2a54..c8bc473c552 100644
--- a/lib/spack/spack/cmd/stage.py
+++ b/lib/spack/spack/cmd/stage.py
@@ -37,13 +37,6 @@ def setup_parser(subparser):
         help="Do not check downloaded packages against checksum")
 
     dir_parser = subparser.add_mutually_exclusive_group()
-    dir_parser.add_argument(
-        '-d', '--print-stage-dir', action='store_const', dest='print_dir',
-        const='print_stage', help="Prints out the stage directory for a spec.")
-    dir_parser.add_argument(
-        '-b', '--print-build-dir', action='store_const', dest='print_dir',
-        const='print_build', help="Prints out the expanded archive path for a spec.")
-
     subparser.add_argument(
         'specs', nargs=argparse.REMAINDER, help="specs of packages to stage")
 
@@ -56,24 +49,7 @@ def stage(parser, args):
         spack.do_checksum = False
 
     specs = spack.cmd.parse_specs(args.specs, concretize=True)
-
-    if args.print_dir:
-        if len(specs) != 1:
-            tty.die("--print-stage-dir and --print-build-dir options only take one spec.")
-
-        spec = specs[0]
-        pkg = spack.db.get(spec)
-
-        if args.print_dir == 'print_stage':
-            print pkg.stage.path
-        elif args.print_dir == 'print_build':
-            if not os.listdir(pkg.stage.path):
-                tty.die("Stage directory is empty.  Run this first:",
-                        "spack stage " + " ".join(args.specs))
-            print pkg.stage.expanded_archive_path
-
-    else:
-        for spec in specs:
-            package = spack.db.get(spec)
-            package.do_stage()
+    for spec in specs:
+        package = spack.db.get(spec)
+        package.do_stage()
 
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 5d2105e37c0..755e9ea9004 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -64,10 +64,10 @@
 def print_help():
     """For use by commands to tell user how to activate shell support."""
 
-    tty.msg("Spack module/dotkit support is not initialized.",
+    tty.msg("This command requires spack's shell integration.",
             "",
-            "To use dotkit or modules with Spack, you must first run",
-            "one of the commands below.  You can copy/paste them.",
+            "To initialize spack's shell commands, you must run one of",
+            "the commands below.  Choose the right command for your shell.",
             "",
             "For bash and zsh:",
             "    . %s/setup-env.sh" % spack.share_path,
diff --git a/share/spack/csh/spack_pathadd.csh b/share/spack/csh/pathadd.csh
similarity index 100%
rename from share/spack/csh/spack_pathadd.csh
rename to share/spack/csh/pathadd.csh
diff --git a/share/spack/csh/spack.csh b/share/spack/csh/spack.csh
index 60736733332..30c4ec13618 100644
--- a/share/spack/csh/spack.csh
+++ b/share/spack/csh/spack.csh
@@ -45,9 +45,9 @@ set _sp_spec=""
 # Figure out what type of module we're running here.
 set _sp_modtype = ""
 switch ($_sp_subcommand)
-case "cd":
+case cd:
     shift _sp_args
-    cd `spack stage --print-build-dir $_sp_args`
+    cd `spack location $_sp_args`
     breaksw
 case use:
 case unuse:
@@ -59,30 +59,36 @@ case unload:
         shift _sp_spec
         set _sp_spec = ($_sp_spec)
     endif
-    # Translate the parameter into pieces of a command.
-    # _sp_modtype is an arg to spack module find, and
-    # _sp_sh_cmd is the equivalent shell command.
-    switch ($_sp_subcommand)
-        case use:
-        case unuse:
-            set _sp_modtype = dotkit
-            set _sp_sh_cmd = ( "`alias $_sp_subcommand'" )
-            breaksw
-        case load:
-        case unload:
-            set _sp_modtype = tcl
-            set _sp_sh_cmd = ( "`alias module`" $_sp_subcommand )
-            breaksw
-    endsw
 
     # Here the user has run use or unuse with a spec.  Find a matching
     # spec using 'spack module find', then use the appropriate module
     # tool's commands to add/remove the result from the environment.
-    # If spack module command comes back with an error, do nothing.
-    set _sp_full_spec = ""
-    if { set _sp_full_spec = `\spack module find $_sp_modtype $_sp_spec` } then
-         $_sp_sh_cmd $_sp_module_args $_sp_full_spec
-    endif
+    switch ($_sp_subcommand)
+        case "use":
+            set _sp_full_spec = ( "`\spack $_sp_flags module find 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`" )
+            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`" )
+            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`" )
+            if ( $? == 0 ) then
+                module unload $_sp_module_args $_sp_full_spec
+            endif
+            breaksw
+    endsw
     breaksw
 
 default:
diff --git a/share/spack/setup-env.csh b/share/spack/setup-env.csh
index cc12eae82f5..5f91670a60d 100755
--- a/share/spack/setup-env.csh
+++ b/share/spack/setup-env.csh
@@ -37,7 +37,7 @@ if ($?SPACK_ROOT) then
 
     # Command aliases point at separate source files
     alias spack          'set _sp_args = (\!*); source $_spack_share_dir/csh/spack.csh'
-    alias _spack_pathadd 'set _pa_args = (\!*) && source $_spack_share_dir/csh/spack_pathadd.csh'
+    alias _spack_pathadd 'set _pa_args = (\!*) && source $_spack_share_dir/csh/pathadd.csh'
 
     # Set up modules and dotkit search paths in the user environment
     # TODO: fix SYS_TYPE to something non-LLNL-specific
diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh
index 9a6090a93b3..6f56d4739b8 100755
--- a/share/spack/setup-env.sh
+++ b/share/spack/setup-env.sh
@@ -76,7 +76,7 @@ function spack {
     # command.
     case $_sp_subcommand in
         "cd")
-            cd $(spack stage --print-build-dir "$@")
+            cd $(spack location "$@")
             return
             ;;
         "use"|"unuse"|"load"|"unload")
@@ -87,28 +87,28 @@ function spack {
                 _sp_spec="$@"
             fi
 
-            # Translate the parameter into pieces of a command.
-            # _sp_modtype is an arg to spack module find, and
-            # _sp_sh_cmd is the equivalent shell command.
-            case $_sp_subcommand in
-                "use"|"unuse")
-                    _sp_modtype=dotkit
-                    _sp_sh_cmd=$_sp_subcommand
-                    ;;
-                "load"|"unload")
-                    _sp_modtype=tcl
-                    _sp_sh_cmd="module $_sp_subcommand"
-                    ;;
-            esac
-
             # Here the user has run use or unuse with a spec.  Find a matching
             # spec using 'spack module find', then use the appropriate module
             # tool's commands to add/remove the result from the environment.
             # If spack module command comes back with an error, do nothing.
-            if _sp_full_spec=$(command spack $_sp_flags module find $_sp_modtype $_sp_spec); then
-                $_sp_sh_cmd $_sp_module_args $_sp_full_spec
-            fi
-            return
+            case $_sp_subcommand in
+                "use")
+                    if _sp_full_spec=$(command spack $_sp_flags module find dotkit $_sp_spec); then
+                        use $_sp_module_args $_sp_full_spec
+                    fi ;;
+                "unuse")
+                    if _sp_full_spec=$(command spack $_sp_flags module find dotkit $_sp_spec); then
+                        unuse $_sp_module_args $_sp_full_spec
+                    fi ;;
+                "load")
+                    if _sp_full_spec=$(command spack $_sp_flags module find dotkit $_sp_spec); then
+                        module load $_sp_module_args $_sp_full_spec
+                    fi ;;
+                "unload")
+                    if _sp_full_spec=$(command spack $_sp_flags module find dotkit $_sp_spec); then
+                        module unload $_sp_module_args $_sp_full_spec
+                    fi ;;
+            esac
             ;;
         *)
             command spack $_sp_flags $_sp_subcommand $_sp_spec

From 42ca6c8bfc2b7598acd880a013f7898db5245004 Mon Sep 17 00:00:00 2001
From: David Beckingsale <davidbeckingsale@gmail.com>
Date: Fri, 22 Aug 2014 13:52:30 -0700
Subject: [PATCH 59/71] Add dependency prefixes to CMAKE_PREFIX_PATH

---
 lib/spack/spack/build_environment.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 38d5f70282d..ec946cd2d73 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -143,6 +143,10 @@ def set_build_environment_variables(pkg):
     os.environ[SPACK_SPEC] = str(pkg.spec)
     os.environ[SPACK_DEBUG_LOG_DIR] = spack.spack_working_dir
 
+    # Add dependencies to CMAKE_PREFIX_PATH
+    dep_prefixes = [d.package.prefix for d in pkg.spec.dependencies.values()]
+    path_set("CMAKE_PREFIX_PATH", dep_prefixes)
+
 
 def set_module_variables_for_package(pkg):
     """Populate the module scope of install() with some useful functions.

From ec44791aa3b5583036f469137412fd40caf11b24 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Fri, 5 Sep 2014 10:52:43 -0700
Subject: [PATCH 60/71] Remove examples from default STAT build to avoid MPI
 dependence.

---
 var/spack/packages/stat/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/packages/stat/package.py b/var/spack/packages/stat/package.py
index 583ae48e82e..956b0dcc8cb 100644
--- a/var/spack/packages/stat/package.py
+++ b/var/spack/packages/stat/package.py
@@ -20,6 +20,7 @@ def install(self, spec, prefix):
         configure(
             "--enable-gui",
             "--prefix=%s" % prefix,
+            "--disable-examples", # Examples require MPI: avoid this dependency.
             "--with-launchmon=%s"   % spec['launchmon'].prefix,
             "--with-mrnet=%s"       % spec['mrnet'].prefix,
             "--with-graphlib=%s"    % spec['graphlib'].prefix,

From 656cf12cdac9bbfdcb583b29eb5d287c430ef6d6 Mon Sep 17 00:00:00 2001
From: Adam Moody <moody20@llnl.gov>
Date: Tue, 16 Sep 2014 16:50:54 -0700
Subject: [PATCH 61/71] add adeptutils and callpath packages

---
 var/spack/packages/adeptutils/package.py | 40 ++++++++++++++++++++++++
 var/spack/packages/callpath/package.py   | 12 +++++--
 2 files changed, 49 insertions(+), 3 deletions(-)
 create mode 100644 var/spack/packages/adeptutils/package.py

diff --git a/var/spack/packages/adeptutils/package.py b/var/spack/packages/adeptutils/package.py
new file mode 100644
index 00000000000..41bf7882dbe
--- /dev/null
+++ b/var/spack/packages/adeptutils/package.py
@@ -0,0 +1,40 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 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 Adeptutils(Package):
+    """LLNL Utility Libraries"""
+
+    homepage = "https://github.com/scalability-llnl/adept-utils"
+    url      = "https://github.com/scalability-llnl/adept-utils/archive/v1.0.tar.gz"
+
+    version('1.0', '5c6cd9badce56c945ac8551e34804397')
+
+    depends_on("mpi")
+
+    def install(self, spec, prefix):
+        cmake("-DCMAKE_INSTALL_PREFIX=" + prefix)
+        make()
+        make("install")
diff --git a/var/spack/packages/callpath/package.py b/var/spack/packages/callpath/package.py
index 5d92d773026..3cbfc26060f 100644
--- a/var/spack/packages/callpath/package.py
+++ b/var/spack/packages/callpath/package.py
@@ -25,13 +25,19 @@
 from spack import *
 
 class Callpath(Package):
-    homepage = "https://github.com/tgamblin/callpath"
-    url      = "http://github.com/tgamblin/callpath-0.2.tar.gz"
+    """Library for representing callpaths consistently in distributed-memory performance tools."""
+
+    homepage = "https://github.com/scalability-llnl/callpath"
+    url      = "https://github.com/scalability-llnl/callpath/archive/v1.0.1.tar.gz"
+
+    version('1.0.1', '0047983d2a52c5c335f8ba7f5bab2325')
 
     depends_on("dyninst")
+    depends_on("adeptutils")
     depends_on("mpi")
 
     def install(self, spec, prefix):
-        configure("--prefix=" + prefix)
+        cmake("-DCMAKE_INSTALL_PREFIX=" + prefix,
+              "-DCALLPATH_WALKER=dyninst")
         make()
         make("install")

From a4c8e945c730d9028f90bb941eec98352fe6504e Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 16 Sep 2014 21:52:39 -0700
Subject: [PATCH 62/71] Some fixups for Adam's callpath and adept-utils
 packages.

- Make spack packages RPATH *ALL* dependencies (i.e. the whole tree)
- prevents callpath link from finding wrong libelf -- always uses the one dyninst used.
---
 lib/spack/spack/build_environment.py                     | 2 +-
 lib/spack/spack/package.py                               | 2 +-
 lib/spack/spack/util/executable.py                       | 2 +-
 .../packages/{adeptutils => adept-utils}/package.py      | 7 ++++---
 var/spack/packages/callpath/package.py                   | 9 +++++----
 5 files changed, 12 insertions(+), 10 deletions(-)
 rename var/spack/packages/{adeptutils => adept-utils}/package.py (91%)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index ec946cd2d73..182a5629fa7 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -122,7 +122,7 @@ def set_build_environment_variables(pkg):
 
     # Prefixes of all of the package's dependencies go in
     # SPACK_DEPENDENCIES
-    dep_prefixes = [d.package.prefix for d in pkg.spec.dependencies.values()]
+    dep_prefixes = [d.prefix for d in pkg.spec.traverse(root=False)]
     path_set(SPACK_DEPENDENCIES, dep_prefixes)
 
     # Install prefix
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index b0a9dd76b97..3e253286e88 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -773,7 +773,7 @@ def do_uninstall(self, **kwargs):
                 ' '.join(formatted_deps))
 
         self.remove_prefix()
-        tty.msg("Successfully uninstalled %s." % self.spec)
+        tty.msg("Successfully uninstalled %s." % self.spec.short_spec)
 
         # Once everything else is done, run post install hooks
         spack.hooks.post_uninstall(self)
diff --git a/lib/spack/spack/util/executable.py b/lib/spack/spack/util/executable.py
index bc27b258895..923c7c19a5b 100644
--- a/lib/spack/spack/util/executable.py
+++ b/lib/spack/spack/util/executable.py
@@ -121,7 +121,7 @@ def which(name, **kwargs):
 
     for dir in path:
         exe = os.path.join(dir, name)
-        if os.access(exe, os.X_OK):
+        if os.path.isfile(exe) and os.access(exe, os.X_OK):
             return Executable(exe)
 
     if required:
diff --git a/var/spack/packages/adeptutils/package.py b/var/spack/packages/adept-utils/package.py
similarity index 91%
rename from var/spack/packages/adeptutils/package.py
rename to var/spack/packages/adept-utils/package.py
index 41bf7882dbe..2515322ec22 100644
--- a/var/spack/packages/adeptutils/package.py
+++ b/var/spack/packages/adept-utils/package.py
@@ -24,17 +24,18 @@
 ##############################################################################
 from spack import *
 
-class Adeptutils(Package):
-    """LLNL Utility Libraries"""
+class AdeptUtils(Package):
+    """Utility libraries for LLNL performance tools."""
 
     homepage = "https://github.com/scalability-llnl/adept-utils"
     url      = "https://github.com/scalability-llnl/adept-utils/archive/v1.0.tar.gz"
 
     version('1.0', '5c6cd9badce56c945ac8551e34804397')
 
+    depends_on("boost")
     depends_on("mpi")
 
     def install(self, spec, prefix):
-        cmake("-DCMAKE_INSTALL_PREFIX=" + prefix)
+        cmake(*std_cmake_args)
         make()
         make("install")
diff --git a/var/spack/packages/callpath/package.py b/var/spack/packages/callpath/package.py
index 3cbfc26060f..84170d9c9ea 100644
--- a/var/spack/packages/callpath/package.py
+++ b/var/spack/packages/callpath/package.py
@@ -25,7 +25,8 @@
 from spack import *
 
 class Callpath(Package):
-    """Library for representing callpaths consistently in distributed-memory performance tools."""
+    """Library for representing callpaths consistently in
+       distributed-memory performance tools."""
 
     homepage = "https://github.com/scalability-llnl/callpath"
     url      = "https://github.com/scalability-llnl/callpath/archive/v1.0.1.tar.gz"
@@ -33,11 +34,11 @@ class Callpath(Package):
     version('1.0.1', '0047983d2a52c5c335f8ba7f5bab2325')
 
     depends_on("dyninst")
-    depends_on("adeptutils")
+    depends_on("adept-utils")
     depends_on("mpi")
 
     def install(self, spec, prefix):
-        cmake("-DCMAKE_INSTALL_PREFIX=" + prefix,
-              "-DCALLPATH_WALKER=dyninst")
+        # TODO: offer options for the walker used.
+        cmake('.', "-DCALLPATH_WALKER=dyninst", *std_cmake_args)
         make()
         make("install")

From 6c94fc4fd28437da840b5761fd63b53224d2f17c Mon Sep 17 00:00:00 2001
From: Adam Moody <moody20@llnl.gov>
Date: Wed, 17 Sep 2014 12:28:00 -0700
Subject: [PATCH 63/71] added mpileaks (finally!)

---
 var/spack/packages/mpileaks/package.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/var/spack/packages/mpileaks/package.py b/var/spack/packages/mpileaks/package.py
index 3307b9fdee8..4ef866588ce 100644
--- a/var/spack/packages/mpileaks/package.py
+++ b/var/spack/packages/mpileaks/package.py
@@ -25,13 +25,20 @@
 from spack import *
 
 class Mpileaks(Package):
-    homepage = "http://www.llnl.gov"
-    url      = "http://www.llnl.gov/mpileaks-1.0.tar.gz"
+    """Tool to detect and report leaked MPI objects like MPI_Requests and MPI_Datatypes."""
+
+    homepage = "https://github.com/hpc/mpileaks"
+    url      = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
+
+    version('1.0', '8838c574b39202a57d7c2d68692718aa')
 
     depends_on("mpi")
+    depends_on("adept-utils")
     depends_on("callpath")
 
     def install(self, spec, prefix):
-        configure("--prefix=" + prefix)
+        configure("--prefix=" + prefix,
+                  "--with-adept-utils=" + spec['adept-utils'].prefix,
+                  "--with-callpath=" + spec['callpath'].prefix)
         make()
         make("install")

From 31bd1e069ce2267e4dd9859bd3cec231987cedcd Mon Sep 17 00:00:00 2001
From: David Boehme <boehme3@llnl.gov>
Date: Wed, 17 Sep 2014 12:28:33 -0700
Subject: [PATCH 64/71] Add Score-P 1.3 release. Works for gcc, still some
 issues with Intel builds.

---
 var/spack/packages/cube/package.py   |  6 ++--
 var/spack/packages/opari2/package.py | 37 ++++++++++++++++++++
 var/spack/packages/otf2/package.py   |  4 +--
 var/spack/packages/scorep/package.py | 52 +++++++++++++++++++++++-----
 4 files changed, 86 insertions(+), 13 deletions(-)

diff --git a/var/spack/packages/cube/package.py b/var/spack/packages/cube/package.py
index 16babb0b589..d97cd25636c 100644
--- a/var/spack/packages/cube/package.py
+++ b/var/spack/packages/cube/package.py
@@ -17,9 +17,11 @@ class Cube(Package):
     version('4.3TP1', 'a2090fbc7b2ba394bd5c09ba971e237f', 
             url = 'http://apps.fz-juelich.de/scalasca/releases/cube/4.3/dist/cube-4.3-TP1.tar.gz')
 
+    # Using CC as C++ compiler provides quirky workaround for a Score-P build system attempt 
+    # to guess a matching C compiler when configuring scorep-score
     backend_user_provided = """\
 CC=cc
-CXX=c++
+CXX=CC
 F77=f77
 FC=f90
 #CFLAGS=-fPIC
@@ -27,7 +29,7 @@ class Cube(Package):
 """
     frontend_user_provided = """\
 CC_FOR_BUILD=cc
-CXX_FOR_BUILD=c++
+CXX_FOR_BUILD=CC
 F77_FOR_BUILD=f70
 FC_FOR_BUILD=f90
 """
diff --git a/var/spack/packages/opari2/package.py b/var/spack/packages/opari2/package.py
index b5711451956..daaee61e3a3 100644
--- a/var/spack/packages/opari2/package.py
+++ b/var/spack/packages/opari2/package.py
@@ -1,6 +1,7 @@
 # FIXME: Add copyright statement here 
 
 from spack import *
+from contextlib import closing
 
 class Opari2(Package):
     """OPARI2 is a source-to-source instrumentation tool for OpenMP and 
@@ -18,9 +19,45 @@ class Opari2(Package):
 
     version('1.1.2', '9a262c7ca05ff0ab5f7775ae96f3539e')
 
+    backend_user_provided = """\
+CC=cc
+CXX=c++
+F77=f77
+FC=f90
+CFLAGS=-fPIC
+CXXFLAGS=-fPIC
+"""
+    frontend_user_provided = """\
+CC_FOR_BUILD=cc
+CXX_FOR_BUILD=c++
+F77_FOR_BUILD=f70
+FC_FOR_BUILD=f90
+CFLAGS_FOR_BUILD=-fPIC
+CXXFLAGS_FOR_BUILD=-fPIC
+"""
+    mpi_user_provided = """\
+MPICC=mpicc
+MPICXX=mpicxx
+MPIF77=mpif77
+MPIFC=mpif90
+MPI_CFLAGS=-fPIC
+MPI_CXXFLAGS=-fPIC
+"""
+
     def install(self, spec, prefix):
+        # Use a custom compiler configuration, otherwise the score-p
+        # build system messes with spack's compiler settings.
+        # Create these three files in the build directory
+        with closing(open("platform-backend-user-provided", "w")) as backend_file:
+            backend_file.write(self.backend_user_provided)
+        with closing(open("platform-frontend-user-provided", "w")) as frontend_file:
+            frontend_file.write(self.frontend_user_provided)
+        with closing(open("platform-mpi-user-provided", "w")) as mpi_file:
+            mpi_file.write(self.mpi_user_provided)            
+
         # FIXME: Modify the configure line to suit your build system here.
         configure("--prefix=%s" % prefix,
+                  "--with-custom-compilers",
                   "--enable-shared")
 
         # FIXME: Add logic to build and install here
diff --git a/var/spack/packages/otf2/package.py b/var/spack/packages/otf2/package.py
index 6f4ab997af1..fa0a5898b6d 100644
--- a/var/spack/packages/otf2/package.py
+++ b/var/spack/packages/otf2/package.py
@@ -43,9 +43,9 @@ class Otf2(Package):
 MPI_CXXFLAGS=-fPIC
 """
 
-    @when('@:1.2')
+    @when('@:1.2.1')
     def version_specific_args(self):
-        return ["--with-platform=disabled"]
+        return ["--with-platform=disabled", "CC=cc", "CXX=c++", "F77=f77", "F90=f90", "CFLAGS=-fPIC", "CXXFLAGS=-fPIC"]
 
     @when('@1.3:')
     def version_specific_args(self):
diff --git a/var/spack/packages/scorep/package.py b/var/spack/packages/scorep/package.py
index 5c42cfdbf2a..32a772e3dbe 100644
--- a/var/spack/packages/scorep/package.py
+++ b/var/spack/packages/scorep/package.py
@@ -1,6 +1,7 @@
 # FIXME: Add copyright statement
 
 from spack import *
+from contextlib import closing
 
 class Scorep(Package):
     """The Score-P measurement infrastructure is a highly scalable and 
@@ -11,16 +12,56 @@ class Scorep(Package):
     homepage = "http://www.vi-hps.org/projects/score-p"
     url      = "http://www.vi-hps.org/upload/packages/scorep/scorep-1.2.3.tar.gz"
 
+    version('1.3', '9db6f957b7f51fa01377a9537867a55c',
+            url = 'http://www.vi-hps.org/upload/packages/scorep/scorep-1.3.tar.gz')
+
     version('1.2.3', '4978084e7cbd05b94517aa8beaea0817')
 
     depends_on("mpi")
     depends_on("papi")
-    depends_on("otf2@1.2:1.2.1") 
+    # depends_on("otf2@1.2:1.2.1") # only Score-P 1.2.x
+    depends_on("otf2") 
     depends_on("opari2")
-    depends_on("cube")
+    depends_on("cube@4.2:4.2.3")
+
+    backend_user_provided = """\
+CC=cc
+CXX=c++
+F77=f77
+FC=f90
+CFLAGS=-fPIC
+CXXFLAGS=-fPIC
+"""
+    frontend_user_provided = """\
+CC_FOR_BUILD=cc
+CXX_FOR_BUILD=c++
+F77_FOR_BUILD=f70
+FC_FOR_BUILD=f90
+CFLAGS_FOR_BUILD=-fPIC
+CXXFLAGS_FOR_BUILD=-fPIC
+"""
+    mpi_user_provided = """\
+MPICC=mpicc
+MPICXX=mpicxx
+MPIF77=mpif77
+MPIFC=mpif90
+MPI_CFLAGS=-fPIC
+MPI_CXXFLAGS=-fPIC
+"""
 
     def install(self, spec, prefix):
+        # Use a custom compiler configuration, otherwise the score-p
+        # build system messes with spack's compiler settings.
+        # Create these three files in the build directory
+        with closing(open("platform-backend-user-provided", "w")) as backend_file:
+            backend_file.write(self.backend_user_provided)
+        with closing(open("platform-frontend-user-provided", "w")) as frontend_file:
+            frontend_file.write(self.frontend_user_provided)
+        with closing(open("platform-mpi-user-provided", "w")) as mpi_file:
+            mpi_file.write(self.mpi_user_provided)            
+
         configure_args = ["--prefix=%s" % prefix,
+                          "--with-custom-compilers",
                           "--with-otf2=%s" % spec['otf2'].prefix.bin,
                           "--with-opari2=%s" % spec['opari2'].prefix.bin,
                           "--with-cube=%s" % spec['cube'].prefix.bin,
@@ -28,13 +69,6 @@ def install(self, spec, prefix):
                           "--with-papi-lib=%s" % spec['papi'].prefix.lib,
                           "--enable-shared"]
 
-        if spec.satisfies('%gcc'):
-            configure_args.append('--with-nocross-compiler-suite=gcc')
-        if spec.satisfies('%intel'):
-            configure_args.append('--with-nocross-compiler-suite=intel')
-        if spec.satisfies('%pgi'):
-            configure_args.append('--with-nocross-compiler-suite=pgi')
-
         configure(*configure_args)
 
         make()

From 68274ee657ce6c430a3c9da45a2986c1ba673a08 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 17 Sep 2014 15:48:13 -0700
Subject: [PATCH 65/71] Add command to show packages added in particular git
 revisions.

spack pkg list    [rev]           list packages for revision.
spack pkg diff    [rev1] [rev2]   diff bt/w packages in rev1 and rev2
spack pkg added   [rev1] [rev2]   pkgs added since rev1
spack pkg removed [rev1] [rev2]   pkgs removed since rev2
---
 lib/spack/spack/cmd/pkg.py | 124 +++++++++++++++++++++++++++++++++++++
 1 file changed, 124 insertions(+)
 create mode 100644 lib/spack/spack/cmd/pkg.py

diff --git a/lib/spack/spack/cmd/pkg.py b/lib/spack/spack/cmd/pkg.py
new file mode 100644
index 00000000000..82ebd13ff92
--- /dev/null
+++ b/lib/spack/spack/cmd/pkg.py
@@ -0,0 +1,124 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 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 os
+
+from external import argparse
+import llnl.util.tty as tty
+from llnl.util.tty.colify import colify
+
+import spack
+from spack.util.executable import *
+
+description = "Query packages associated with particular git revisions in spack."
+
+def setup_parser(subparser):
+    sp = subparser.add_subparsers(
+        metavar='SUBCOMMAND', dest='pkg_command')
+
+    list_parser = sp.add_parser('list', help=pkg_list.__doc__)
+    list_parser.add_argument('rev', default='HEAD', nargs='?',
+                             help="Revision to list packages for.")
+
+    diff_parser = sp.add_parser('diff', help=pkg_diff.__doc__)
+    diff_parser.add_argument('rev1', nargs='?', default='HEAD^',
+                             help="Revision to compare against.")
+    diff_parser.add_argument('rev2', nargs='?', default='HEAD',
+                             help="Revision to compare to rev1 (default is HEAD).")
+
+    add_parser = sp.add_parser('added', help=pkg_added.__doc__)
+    add_parser.add_argument('rev1', nargs='?', default='HEAD^',
+                             help="Revision to compare against.")
+    add_parser.add_argument('rev2', nargs='?', default='HEAD',
+                            help="Revision to compare to rev1 (default is HEAD).")
+
+    rm_parser = sp.add_parser('removed', help=pkg_removed.__doc__)
+    rm_parser.add_argument('rev1', nargs='?', default='HEAD^',
+                           help="Revision to compare against.")
+    rm_parser.add_argument('rev2', nargs='?', default='HEAD',
+                           help="Revision to compare to rev1 (default is HEAD).")
+
+
+def get_git():
+    # cd to spack prefix to do git operations
+    os.chdir(spack.prefix)
+
+    # If this is a non-git version of spack, give up.
+    if not os.path.isdir('.git'):
+        tty.die("No git repo in %s. Can't use 'spack pkg'" % spack.prefix)
+
+    return which("git", required=True)
+
+
+def list_packages(rev):
+    git = get_git()
+    relpath = spack.packages_path[len(spack.prefix + os.path.sep):] + os.path.sep
+    output = git('ls-tree', '--full-tree', '--name-only', rev, relpath,
+                 return_output=True)
+    return sorted(line[len(relpath):] for line in output.split('\n') if line)
+
+
+def pkg_list(args):
+    """List packages associated with a particular spack git revision."""
+    colify(list_packages(args.rev))
+
+
+def diff_packages(rev1, rev2):
+    p1 = set(list_packages(rev1))
+    p2 = set(list_packages(rev2))
+    return p1.difference(p2), p2.difference(p1)
+
+
+def pkg_diff(args):
+    """Compare packages available in two different git revisions."""
+    u1, u2 = diff_packages(args.rev1, args.rev2)
+
+    if u1:
+        print "%s:" % args.rev1
+        colify(sorted(u1), indent=4)
+        if u1: print
+
+    if u2:
+        print "%s:" % args.rev2
+        colify(sorted(u2), indent=4)
+
+
+def pkg_removed(args):
+    """Show packages removed since a commit."""
+    u1, u2 = diff_packages(args.rev1, args.rev2)
+    if u1: colify(sorted(u1))
+
+
+def pkg_added(args):
+    """Show packages added since a commit."""
+    u1, u2 = diff_packages(args.rev1, args.rev2)
+    if u2: colify(sorted(u2))
+
+
+def pkg(parser, args):
+    action = { 'diff'    : pkg_diff,
+               'list'    : pkg_list,
+               'removed' : pkg_removed,
+               'added'   : pkg_added }
+    action[args.pkg_command](args)

From 8c4db76c3a32efdb1527da4534c80df8d9489b2c Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 17 Sep 2014 15:48:13 -0700
Subject: [PATCH 66/71] Add command to show packages added in particular git
 revisions.

spack pkg list    [rev]           list packages for revision.
spack pkg diff    [rev1] [rev2]   diff bt/w packages in rev1 and rev2
spack pkg added   [rev1] [rev2]   pkgs added since rev1
spack pkg removed [rev1] [rev2]   pkgs removed since rev2
---
 lib/spack/spack/cmd/pkg.py | 124 +++++++++++++++++++++++++++++++++++++
 1 file changed, 124 insertions(+)
 create mode 100644 lib/spack/spack/cmd/pkg.py

diff --git a/lib/spack/spack/cmd/pkg.py b/lib/spack/spack/cmd/pkg.py
new file mode 100644
index 00000000000..82ebd13ff92
--- /dev/null
+++ b/lib/spack/spack/cmd/pkg.py
@@ -0,0 +1,124 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 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 os
+
+from external import argparse
+import llnl.util.tty as tty
+from llnl.util.tty.colify import colify
+
+import spack
+from spack.util.executable import *
+
+description = "Query packages associated with particular git revisions in spack."
+
+def setup_parser(subparser):
+    sp = subparser.add_subparsers(
+        metavar='SUBCOMMAND', dest='pkg_command')
+
+    list_parser = sp.add_parser('list', help=pkg_list.__doc__)
+    list_parser.add_argument('rev', default='HEAD', nargs='?',
+                             help="Revision to list packages for.")
+
+    diff_parser = sp.add_parser('diff', help=pkg_diff.__doc__)
+    diff_parser.add_argument('rev1', nargs='?', default='HEAD^',
+                             help="Revision to compare against.")
+    diff_parser.add_argument('rev2', nargs='?', default='HEAD',
+                             help="Revision to compare to rev1 (default is HEAD).")
+
+    add_parser = sp.add_parser('added', help=pkg_added.__doc__)
+    add_parser.add_argument('rev1', nargs='?', default='HEAD^',
+                             help="Revision to compare against.")
+    add_parser.add_argument('rev2', nargs='?', default='HEAD',
+                            help="Revision to compare to rev1 (default is HEAD).")
+
+    rm_parser = sp.add_parser('removed', help=pkg_removed.__doc__)
+    rm_parser.add_argument('rev1', nargs='?', default='HEAD^',
+                           help="Revision to compare against.")
+    rm_parser.add_argument('rev2', nargs='?', default='HEAD',
+                           help="Revision to compare to rev1 (default is HEAD).")
+
+
+def get_git():
+    # cd to spack prefix to do git operations
+    os.chdir(spack.prefix)
+
+    # If this is a non-git version of spack, give up.
+    if not os.path.isdir('.git'):
+        tty.die("No git repo in %s. Can't use 'spack pkg'" % spack.prefix)
+
+    return which("git", required=True)
+
+
+def list_packages(rev):
+    git = get_git()
+    relpath = spack.packages_path[len(spack.prefix + os.path.sep):] + os.path.sep
+    output = git('ls-tree', '--full-tree', '--name-only', rev, relpath,
+                 return_output=True)
+    return sorted(line[len(relpath):] for line in output.split('\n') if line)
+
+
+def pkg_list(args):
+    """List packages associated with a particular spack git revision."""
+    colify(list_packages(args.rev))
+
+
+def diff_packages(rev1, rev2):
+    p1 = set(list_packages(rev1))
+    p2 = set(list_packages(rev2))
+    return p1.difference(p2), p2.difference(p1)
+
+
+def pkg_diff(args):
+    """Compare packages available in two different git revisions."""
+    u1, u2 = diff_packages(args.rev1, args.rev2)
+
+    if u1:
+        print "%s:" % args.rev1
+        colify(sorted(u1), indent=4)
+        if u1: print
+
+    if u2:
+        print "%s:" % args.rev2
+        colify(sorted(u2), indent=4)
+
+
+def pkg_removed(args):
+    """Show packages removed since a commit."""
+    u1, u2 = diff_packages(args.rev1, args.rev2)
+    if u1: colify(sorted(u1))
+
+
+def pkg_added(args):
+    """Show packages added since a commit."""
+    u1, u2 = diff_packages(args.rev1, args.rev2)
+    if u2: colify(sorted(u2))
+
+
+def pkg(parser, args):
+    action = { 'diff'    : pkg_diff,
+               'list'    : pkg_list,
+               'removed' : pkg_removed,
+               'added'   : pkg_added }
+    action[args.pkg_command](args)

From 250ffc28a3f94d039829cb96078a8242086e7dd5 Mon Sep 17 00:00:00 2001
From: Adam Moody <moody20@llnl.gov>
Date: Wed, 17 Sep 2014 23:40:16 -0700
Subject: [PATCH 67/71] update libcircle to download tarball from github/hpc

---
 var/spack/packages/libcircle/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/packages/libcircle/package.py b/var/spack/packages/libcircle/package.py
index e398125328a..3f7c996fb05 100644
--- a/var/spack/packages/libcircle/package.py
+++ b/var/spack/packages/libcircle/package.py
@@ -6,9 +6,9 @@ class Libcircle(Package):
        using self-stabilizing work stealing."""
 
     homepage = "https://github.com/hpc/libcircle"
-    url      = "https://github.com/adammoody/libcircle/releases/download/v0.2.1-rc.1/libcircle-0.2.1-rc.1.tar.gz"
 
-    version('0.2.1-rc.1', 'a10a14e76ac2ad7357a4b21b794e8e4e')
+    version('0.2.1-rc.1', '2b1369a5736457239f908abf88143ec2',
+             url='https://github.com/hpc/libcircle/releases/download/0.2.1-rc.1/libcircle-0.2.1-rc.1.tar.gz')
 
     depends_on('mpi')
 

From 4a19fa793edb524e0b77717c4eb25b4e958020bc Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 18 Sep 2014 01:42:01 -0700
Subject: [PATCH 68/71] Support for pkg-config.

---
 lib/spack/spack/build_environment.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 182a5629fa7..94d5b7a3bee 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -144,9 +144,17 @@ def set_build_environment_variables(pkg):
     os.environ[SPACK_DEBUG_LOG_DIR] = spack.spack_working_dir
 
     # Add dependencies to CMAKE_PREFIX_PATH
-    dep_prefixes = [d.package.prefix for d in pkg.spec.dependencies.values()]
     path_set("CMAKE_PREFIX_PATH", dep_prefixes)
 
+    # Add any pkgconfig directories to PKG_CONFIG_PATH
+    pkg_config_dirs = []
+    for p in dep_prefixes:
+        for libdir in ('lib', 'lib64'):
+            pcdir = join_path(p, libdir, 'pkgconfig')
+            if os.path.isdir(pcdir):
+                pkg_config_dirs.append(pcdir)
+    path_set("PKG_CONFIG_PATH", pkg_config_dirs)
+
 
 def set_module_variables_for_package(pkg):
     """Populate the module scope of install() with some useful functions.

From e85830e3133b793d6da32c8d546a2f8d15d220d9 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 18 Sep 2014 01:49:30 -0700
Subject: [PATCH 69/71] Fileutils successfully finds libarchive; can't find
 dtcmp despite config arg.

---
 var/spack/packages/fileutils/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/packages/fileutils/package.py b/var/spack/packages/fileutils/package.py
index 449ed0c72e7..73398a826c5 100644
--- a/var/spack/packages/fileutils/package.py
+++ b/var/spack/packages/fileutils/package.py
@@ -8,7 +8,7 @@ class Fileutils(Package):
     homepage = "https://github.com/hpc/fileutils"
     url      = "https://github.com/hpc/fileutils/releases/download/v0.0.1-alpha.4/fileutils-0.0.1-alpha.4.tar.gz"
 
-    version('0.0.1-alpha.4', 'a01dbe5a2e03f3c70c7a98ec0a2554e1')
+    version('0.0.1-alpha.4', 'e37b48ea43c95f5a1ede0ee01019ae58')
 
     depends_on('mpi')
     depends_on('libcircle')
@@ -17,6 +17,6 @@ class Fileutils(Package):
 
     def install(self, spec, prefix):
         configure("--prefix=" + prefix,
-                  "--with-libdtcmp=" + spec['dtcmp'].prefix)
+                  "--with-dtcmp=" + spec['dtcmp'].prefix)
         make()
         make("install")

From 4d2ccfa02842eb152cf7a9bfd3e91cde6e8c6816 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 18 Sep 2014 21:33:09 -0700
Subject: [PATCH 70/71] Take fileutils out and just merge the deps into
 develop.

---
 var/spack/packages/fileutils/package.py | 22 ----------------------
 1 file changed, 22 deletions(-)
 delete mode 100644 var/spack/packages/fileutils/package.py

diff --git a/var/spack/packages/fileutils/package.py b/var/spack/packages/fileutils/package.py
deleted file mode 100644
index 73398a826c5..00000000000
--- a/var/spack/packages/fileutils/package.py
+++ /dev/null
@@ -1,22 +0,0 @@
-import os
-from spack import *
-
-class Fileutils(Package):
-    """FileUtils provides a suite of MPI-based tools to manage large files
-       and datasets on parallel file systems."""
-
-    homepage = "https://github.com/hpc/fileutils"
-    url      = "https://github.com/hpc/fileutils/releases/download/v0.0.1-alpha.4/fileutils-0.0.1-alpha.4.tar.gz"
-
-    version('0.0.1-alpha.4', 'e37b48ea43c95f5a1ede0ee01019ae58')
-
-    depends_on('mpi')
-    depends_on('libcircle')
-    depends_on('libarchive')
-    depends_on('dtcmp')
-
-    def install(self, spec, prefix):
-        configure("--prefix=" + prefix,
-                  "--with-dtcmp=" + spec['dtcmp'].prefix)
-        make()
-        make("install")

From 9165a000a3b0ac68692d8ad58bb41d85276cec61 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 18 Sep 2014 23:22:03 -0700
Subject: [PATCH 71/71] Better C++11 support, remove non-standalone
 llvm-compiler-rt.

- LLVM non-standalone add-ons are difficult to build outside LLVM.
- May have to wait for future versions of LLVM to build some of these
---
 lib/spack/spack/build_environment.py          |   2 +-
 lib/spack/spack/cmd/pkg.py                    | 124 ++++++++++++++++++
 lib/spack/spack/compiler.py                   |   3 +
 lib/spack/spack/compilers/gcc.py              |  11 ++
 lib/spack/spack/compilers/intel.py            |   9 ++
 lib/spack/spack/package.py                    |   9 ++
 var/spack/packages/clang/package.py           |   2 +-
 .../packages/llvm-compiler-rt/package.py      |  57 --------
 var/spack/packages/llvm-lld/package.py        |   4 +-
 var/spack/packages/llvm/package.py            |   2 +-
 10 files changed, 161 insertions(+), 62 deletions(-)
 create mode 100644 lib/spack/spack/cmd/pkg.py
 delete mode 100644 var/spack/packages/llvm-compiler-rt/package.py

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index f72c7244200..80abde70a95 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -84,7 +84,7 @@ def __call__(self, *args, **kwargs):
 
 def set_compiler_environment_variables(pkg):
     assert(pkg.spec.concrete)
-    compiler = compilers.compiler_for_spec(pkg.spec.compiler)
+    compiler = pkg.compiler
 
     # Set compiler variables used by CMake and autotools
     os.environ['CC']  = 'cc'
diff --git a/lib/spack/spack/cmd/pkg.py b/lib/spack/spack/cmd/pkg.py
new file mode 100644
index 00000000000..82ebd13ff92
--- /dev/null
+++ b/lib/spack/spack/cmd/pkg.py
@@ -0,0 +1,124 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
+# the Free Software Foundation) version 2.1 dated 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 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 os
+
+from external import argparse
+import llnl.util.tty as tty
+from llnl.util.tty.colify import colify
+
+import spack
+from spack.util.executable import *
+
+description = "Query packages associated with particular git revisions in spack."
+
+def setup_parser(subparser):
+    sp = subparser.add_subparsers(
+        metavar='SUBCOMMAND', dest='pkg_command')
+
+    list_parser = sp.add_parser('list', help=pkg_list.__doc__)
+    list_parser.add_argument('rev', default='HEAD', nargs='?',
+                             help="Revision to list packages for.")
+
+    diff_parser = sp.add_parser('diff', help=pkg_diff.__doc__)
+    diff_parser.add_argument('rev1', nargs='?', default='HEAD^',
+                             help="Revision to compare against.")
+    diff_parser.add_argument('rev2', nargs='?', default='HEAD',
+                             help="Revision to compare to rev1 (default is HEAD).")
+
+    add_parser = sp.add_parser('added', help=pkg_added.__doc__)
+    add_parser.add_argument('rev1', nargs='?', default='HEAD^',
+                             help="Revision to compare against.")
+    add_parser.add_argument('rev2', nargs='?', default='HEAD',
+                            help="Revision to compare to rev1 (default is HEAD).")
+
+    rm_parser = sp.add_parser('removed', help=pkg_removed.__doc__)
+    rm_parser.add_argument('rev1', nargs='?', default='HEAD^',
+                           help="Revision to compare against.")
+    rm_parser.add_argument('rev2', nargs='?', default='HEAD',
+                           help="Revision to compare to rev1 (default is HEAD).")
+
+
+def get_git():
+    # cd to spack prefix to do git operations
+    os.chdir(spack.prefix)
+
+    # If this is a non-git version of spack, give up.
+    if not os.path.isdir('.git'):
+        tty.die("No git repo in %s. Can't use 'spack pkg'" % spack.prefix)
+
+    return which("git", required=True)
+
+
+def list_packages(rev):
+    git = get_git()
+    relpath = spack.packages_path[len(spack.prefix + os.path.sep):] + os.path.sep
+    output = git('ls-tree', '--full-tree', '--name-only', rev, relpath,
+                 return_output=True)
+    return sorted(line[len(relpath):] for line in output.split('\n') if line)
+
+
+def pkg_list(args):
+    """List packages associated with a particular spack git revision."""
+    colify(list_packages(args.rev))
+
+
+def diff_packages(rev1, rev2):
+    p1 = set(list_packages(rev1))
+    p2 = set(list_packages(rev2))
+    return p1.difference(p2), p2.difference(p1)
+
+
+def pkg_diff(args):
+    """Compare packages available in two different git revisions."""
+    u1, u2 = diff_packages(args.rev1, args.rev2)
+
+    if u1:
+        print "%s:" % args.rev1
+        colify(sorted(u1), indent=4)
+        if u1: print
+
+    if u2:
+        print "%s:" % args.rev2
+        colify(sorted(u2), indent=4)
+
+
+def pkg_removed(args):
+    """Show packages removed since a commit."""
+    u1, u2 = diff_packages(args.rev1, args.rev2)
+    if u1: colify(sorted(u1))
+
+
+def pkg_added(args):
+    """Show packages added since a commit."""
+    u1, u2 = diff_packages(args.rev1, args.rev2)
+    if u2: colify(sorted(u2))
+
+
+def pkg(parser, args):
+    action = { 'diff'    : pkg_diff,
+               'list'    : pkg_list,
+               'removed' : pkg_removed,
+               'added'   : pkg_added }
+    action[args.pkg_command](args)
diff --git a/lib/spack/spack/compiler.py b/lib/spack/spack/compiler.py
index 716356bdd2a..e4a6629759b 100644
--- a/lib/spack/spack/compiler.py
+++ b/lib/spack/spack/compiler.py
@@ -94,6 +94,9 @@ class Compiler(object):
     # Names of generic arguments used by this compiler
     arg_rpath   = '-Wl,-rpath,%s'
 
+    # argument used to get C++11 options
+    cxx11_flag = "-std=c++11"
+
 
     def __init__(self, cspec, cc, cxx, f77, fc):
         def check(exe):
diff --git a/lib/spack/spack/compilers/gcc.py b/lib/spack/spack/compilers/gcc.py
index cc3c52ca614..097b24bb874 100644
--- a/lib/spack/spack/compilers/gcc.py
+++ b/lib/spack/spack/compilers/gcc.py
@@ -22,7 +22,9 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
+import llnl.util.tty as tty
 from spack.compiler import *
+from spack.version import ver
 
 class Gcc(Compiler):
     # Subclasses use possible names of C compiler
@@ -40,6 +42,15 @@ class Gcc(Compiler):
     # MacPorts builds gcc versions with prefixes and -mp-X.Y suffixes.
     suffixes = [r'-mp-\d\.\d']
 
+    @property
+    def cxx11_flag(self):
+        if self.version < ver('4.3'):
+            tty.die("Only gcc 4.3 and above support c++11.")
+        elif self.version < ver('4.7'):
+            return "-std=gnu++0x"
+        else:
+            return "-std=gnu++11"
+
     @classmethod
     def fc_version(cls, fc):
         return get_compiler_version(
diff --git a/lib/spack/spack/compilers/intel.py b/lib/spack/spack/compilers/intel.py
index 02e3b96b198..2a72c4eaea0 100644
--- a/lib/spack/spack/compilers/intel.py
+++ b/lib/spack/spack/compilers/intel.py
@@ -37,6 +37,15 @@ class Intel(Compiler):
     # Subclasses use possible names of Fortran 90 compiler
     fc_names = ['ifort']
 
+    @property
+    def cxx11_flag(self):
+        if self.version < ver('11.1'):
+            tty.die("Only intel 11.1 and above support c++11.")
+        elif self.version < ver('13'):
+            return "-std=c++0x"
+        else:
+            return "-std=c++11"
+
 
     @classmethod
     def default_version(cls, comp):
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 0375df7dac5..1afdeaf2a02 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -48,6 +48,7 @@
 import spack
 import spack.spec
 import spack.error
+import spack.compilers
 import spack.hooks
 import spack.build_environment as build_env
 import spack.url as url
@@ -505,6 +506,14 @@ def prefix(self):
         return self.spec.prefix
 
 
+    @property
+    def compiler(self):
+        """Get the spack.compiler.Compiler object used to build this package."""
+        if not self.spec.concrete:
+            raise ValueError("Can only get a compiler for a concrete package.")
+        return spack.compilers.compiler_for_spec(self.spec.compiler)
+
+
     def url_version(self, version):
         """Given a version, this returns a string that should be substituted into the
            package's URL to download that version.
diff --git a/var/spack/packages/clang/package.py b/var/spack/packages/clang/package.py
index 07948a3ed72..b0097bd1261 100644
--- a/var/spack/packages/clang/package.py
+++ b/var/spack/packages/clang/package.py
@@ -36,7 +36,7 @@ class Clang(Package):
     version('3.4.2', '87945973b7c73038871c5f849a818588')
 
     def install(self, spec, prefix):
-        env['CXXFLAGS'] = '-std=c++11'
+        env['CXXFLAGS'] = self.compiler.cxx11_flag
 
         with working_dir('spack-build', create=True):
             cmake('..',
diff --git a/var/spack/packages/llvm-compiler-rt/package.py b/var/spack/packages/llvm-compiler-rt/package.py
deleted file mode 100644
index e3fa176afe1..00000000000
--- a/var/spack/packages/llvm-compiler-rt/package.py
+++ /dev/null
@@ -1,57 +0,0 @@
-##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://scalability-llnl.github.io/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 General Public License (as published by
-# the Free Software Foundation) version 2.1 dated 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 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 LlvmCompilerRt(Package):
-    """Compiler-rt consists of several libraries to be used with LLVM:
-          basics:
-              A simple library that provides an implementation of the
-              low-level target-specific hooks required by code
-              generation and other runtime components.
-
-          sanitizer runtimes:
-              Runtime libraries that are required to run the code with
-              sanitizer instrumentation.
-
-          profiler:
-              Library used to collect coverage information.
-
-          BlocksRuntime:
-              A target-independent implementation of Apple "Blocks"
-              runtime interfaces.
-    """
-    homepage = "http://compiler-rt.llvm.org"
-    url      = "http://llvm.org/releases/3.4/compiler-rt-3.4.src.tar.gz"
-
-    depends_on("clang")
-    depends_on("llvm")
-
-    version('3.4', '7938353e3a3bda85733a165e7ac4bb84')
-
-    def install(self, spec, prefix):
-        cmake(".", *std_cmake_args)
-
-        make()
-        make("install")
diff --git a/var/spack/packages/llvm-lld/package.py b/var/spack/packages/llvm-lld/package.py
index ba0b229228e..f2292113962 100644
--- a/var/spack/packages/llvm-lld/package.py
+++ b/var/spack/packages/llvm-lld/package.py
@@ -35,12 +35,12 @@ class LlvmLld(Package):
     version('3.4', '3b6a17e58c8416c869c14dd37682f78e')
 
     def install(self, spec, prefix):
-        env['CXXFLAGS'] = '-std=c++11'
+        env['CXXFLAGS'] = self.compier.cxx11_flag
 
         with working_dir('spack-build', create=True):
             cmake('..',
                   '-DLLD_PATH_TO_LLVM_BUILD=%s' % spec['llvm'].prefix,
                   '-DLLVM_MAIN_SRC_DIR=%s' % spec['llvm'].prefix,
                   *std_cmake_args)
-            make('VERBOSE=1')
+            make()
             make("install")
diff --git a/var/spack/packages/llvm/package.py b/var/spack/packages/llvm/package.py
index 08ae7208cd0..c7a10df55ae 100644
--- a/var/spack/packages/llvm/package.py
+++ b/var/spack/packages/llvm/package.py
@@ -37,7 +37,7 @@ class Llvm(Package):
     version('3.4.2', 'a20669f75967440de949ac3b1bad439c')
 
     def install(self, spec, prefix):
-        env['CXXFLAGS'] = '-std=c++11'
+        env['CXXFLAGS'] = self.compiler.cxx11_flag
 
         with working_dir('spack-build', create=True):
             cmake('..',