Merge branch 'features/python-modules' into develop

69 files changed, 2302 insertions, 111 deletions

diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index 0578415653..576aeb16bd 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -23,7 +23,7 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 __all__ = ['set_install_permissions', 'install', 'expand_user', 'working_dir',
-           'touch', 'mkdirp', 'force_remove', 'join_path', 'ancestor',
+           'touch', 'touchp', 'mkdirp', 'force_remove', 'join_path', 'ancestor',
            'can_access', 'filter_file', 'change_sed_delimiter', 'is_exe']
 
 import os
@@ -204,6 +204,12 @@ def touch(path):
         os.utime(path, None)
 
 
+def touchp(path):
+    """Like touch, but creates any parent directories needed for the file."""
+    mkdirp(os.path.dirname(path))
+    touch(path)
+
+
 def join_path(prefix, *args):
     path = str(prefix)
     for elt in args:
diff --git a/lib/spack/llnl/util/lang.py b/lib/spack/llnl/util/lang.py
index db15da0506..332367f537 100644
--- a/lib/spack/llnl/util/lang.py
+++ b/lib/spack/llnl/util/lang.py
@@ -291,6 +291,37 @@ def check_kwargs(kwargs, fun):
             % (next(kwargs.iterkeys()), fun.__name__))
 
 
+def match_predicate(*args):
+    """Utility function for making string matching predicates.
+
+    Each arg can be a:
+        - regex
+        - list or tuple of regexes
+        - predicate that takes a string.
+
+    This returns a predicate that is true if:
+        - any arg regex matches
+        - any regex in a list or tuple of regexes matches.
+        - any predicate in args matches.
+    """
+    def match(string):
+        for arg in args:
+            if isinstance(arg, basestring):
+                if re.search(arg, string):
+                    return True
+            elif isinstance(arg, list) or isinstance(arg, tuple):
+                if any(re.search(i, string) for i in arg):
+                    return True
+            elif callable(arg):
+                if arg(string):
+                    return True
+            else:
+                raise ValueError("args to match_predicate must be regex, "
+                                 "list of regexes, or callable.")
+        return False
+    return match
+
+
 class RequiredAttributeError(ValueError):
     def __init__(self, message):
         super(RequiredAttributeError, self).__init__(message)
diff --git a/lib/spack/llnl/util/link_tree.py b/lib/spack/llnl/util/link_tree.py
new file mode 100644
index 0000000000..4d778eca1e
--- /dev/null
+++ b/lib/spack/llnl/util/link_tree.py
@@ -0,0 +1,197 @@
+##############################################################################
+# 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
+##############################################################################
+"""LinkTree class for setting up trees of symbolic links."""
+__all__ = ['LinkTree']
+
+import os
+import shutil
+from llnl.util.filesystem import *
+
+empty_file_name = '.spack-empty'
+
+
+def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
+    """Traverse two filesystem trees simultaneously.
+
+    Walks the LinkTree directory in pre or post order.  Yields each
+    file in the source directory with a matching path from the dest
+    directory, along with whether the file is a directory.
+    e.g., for this tree::
+
+        root/
+          a/
+            file1
+            file2
+          b/
+            file3
+
+    When called on dest, this yields::
+
+        ('root',         'dest')
+        ('root/a',       'dest/a')
+        ('root/a/file1', 'dest/a/file1')
+        ('root/a/file2', 'dest/a/file2')
+        ('root/b',       'dest/b')
+        ('root/b/file3', 'dest/b/file3')
+
+    Optional args:
+
+    order=[pre|post] -- Whether to do pre- or post-order traveral.
+
+    ignore=<predicate> -- Predicate indicating which files to ignore.
+
+    follow_nonexisting -- Whether to descend into directories in
+                          src that do not exit in dest. Default True.
+
+    follow_links -- Whether to descend into symlinks in src.
+
+    """
+    follow_nonexisting = kwargs.get('follow_nonexisting', True)
+    follow_links = kwargs.get('follow_link', False)
+
+    # Yield in pre or post order?
+    order  = kwargs.get('order', 'pre')
+    if order not in ('pre', 'post'):
+        raise ValueError("Order must be 'pre' or 'post'.")
+
+    # List of relative paths to ignore under the src root.
+    ignore = kwargs.get('ignore', lambda filename: False)
+
+    # Don't descend into ignored directories
+    if ignore(rel_path):
+        return
+
+    source_path = os.path.join(source_root, rel_path)
+    dest_path   = os.path.join(dest_root, rel_path)
+
+    # preorder yields directories before children
+    if order == 'pre':
+        yield (source_path, dest_path)
+
+    for f in os.listdir(source_path):
+        source_child = os.path.join(source_path, f)
+        dest_child   = os.path.join(dest_path, f)
+        rel_child    = os.path.join(rel_path, f)
+
+        # Treat as a directory
+        if os.path.isdir(source_child) and (
+            follow_links or not os.path.islink(source_child)):
+
+            # When follow_nonexisting isn't set, don't descend into dirs
+            # in source that do not exist in dest
+            if follow_nonexisting or os.path.exists(dest_child):
+                tuples = traverse_tree(source_root, dest_root, rel_child, **kwargs)
+                for t in tuples: yield t
+
+        # Treat as a file.
+        elif not ignore(os.path.join(rel_path, f)):
+            yield (source_child, dest_child)
+
+    if order == 'post':
+        yield (source_path, dest_path)
+
+
+
+class LinkTree(object):
+    """Class to create trees of symbolic links from a source directory.
+
+    LinkTree objects are constructed with a source root.  Their
+    methods allow you to create and delete trees of symbolic links
+    back to the source tree in specific destination directories.
+    Trees comprise symlinks only to files; directries are never
+    symlinked to, to prevent the source directory from ever being
+    modified.
+
+    """
+    def __init__(self, source_root):
+        if not os.path.exists(source_root):
+            raise IOError("No such file or directory: '%s'", source_root)
+
+        self._root = source_root
+
+
+    def find_conflict(self, dest_root, **kwargs):
+        """Returns the first file in dest that conflicts with src"""
+        kwargs['follow_nonexisting'] = False
+        for src, dest in traverse_tree(self._root, dest_root, **kwargs):
+            if os.path.isdir(src):
+                if os.path.exists(dest) and not os.path.isdir(dest):
+                    return dest
+            elif os.path.exists(dest):
+                return dest
+        return None
+
+
+    def merge(self, dest_root, **kwargs):
+        """Link all files in src into dest, creating directories if necessary."""
+        kwargs['order'] = 'pre'
+        for src, dest in traverse_tree(self._root, dest_root, **kwargs):
+            if os.path.isdir(src):
+                if not os.path.exists(dest):
+                    mkdirp(dest)
+                    continue
+
+                if not os.path.isdir(dest):
+                    raise ValueError("File blocks directory: %s" % dest)
+
+                # mark empty directories so they aren't removed on unmerge.
+                if not os.listdir(dest):
+                    marker = os.path.join(dest, empty_file_name)
+                    touch(marker)
+
+            else:
+                assert(not os.path.exists(dest))
+                os.symlink(src, dest)
+
+
+    def unmerge(self, dest_root, **kwargs):
+        """Unlink all files in dest that exist in src.
+
+        Unlinks directories in dest if they are empty.
+
+        """
+        kwargs['order'] = 'post'
+        for src, dest in traverse_tree(self._root, dest_root, **kwargs):
+            if os.path.isdir(src):
+                # Skip non-existing links.
+                if not os.path.exists(dest):
+                    continue
+
+                if not os.path.isdir(dest):
+                    raise ValueError("File blocks directory: %s" % dest)
+
+                # remove directory if it is empty.
+                if not os.listdir(dest):
+                    shutil.rmtree(dest, ignore_errors=True)
+
+                # remove empty dir marker if present.
+                marker = os.path.join(dest, empty_file_name)
+                if os.path.exists(marker):
+                    os.remove(marker)
+
+            elif os.path.exists(dest):
+                if not os.path.islink(dest):
+                    raise ValueError("%s is not a link tree!" % dest)
+                os.remove(dest)
diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py
index 6697e00e40..6763411f7d 100644
--- a/lib/spack/spack/__init__.py
+++ b/lib/spack/spack/__init__.py
@@ -138,7 +138,7 @@ sys_type = None
 #       should live.  This file is overloaded for spack core vs. for packages.
 #
 __all__ = ['Package', 'Version', 'when', 'ver']
-from spack.package import Package
+from spack.package import Package, ExtensionConflictError
 from spack.version import Version, ver
 from spack.multimethod import when
 
diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 45353ec640..84d2bd77ef 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -28,6 +28,7 @@ Skimming this module is a nice way to get acquainted with the types of
 calls you can make from within the install() function.
 """
 import os
+import sys
 import shutil
 import multiprocessing
 import platform
@@ -207,3 +208,63 @@ def setup_package(pkg):
     set_compiler_environment_variables(pkg)
     set_build_environment_variables(pkg)
     set_module_variables_for_package(pkg)
+
+    # Allow dependencies to set up environment as well.
+    for dep_spec in pkg.spec.traverse(root=False):
+        dep_spec.package.setup_dependent_environment(
+            pkg.module, dep_spec, pkg.spec)
+
+
+def fork(pkg, function):
+    """Fork a child process to do part of a spack build.
+
+    Arguments:
+
+    pkg -- pkg whose environemnt we should set up the
+           forked process for.
+    function -- arg-less function to run in the child process.
+
+    Usage:
+       def child_fun():
+           # do stuff
+       build_env.fork(pkg, child_fun)
+
+    Forked processes are run with the build environemnt set up by
+    spack.build_environment.  This allows package authors to have
+    full control over the environment, etc. without offecting
+    other builds that might be executed in the same spack call.
+
+    If something goes wrong, the child process is expected toprint
+    the error and the parent process will exit with error as
+    well. If things go well, the child exits and the parent
+    carries on.
+    """
+    try:
+        pid = os.fork()
+    except OSError, e:
+        raise InstallError("Unable to fork build process: %s" % e)
+
+    if pid == 0:
+        # Give the child process the package's build environemnt.
+        setup_package(pkg)
+
+        try:
+            # call the forked function.
+            function()
+
+            # Use os._exit here to avoid raising a SystemExit exception,
+            # which interferes with unit tests.
+            os._exit(0)
+        except:
+            # Child doesn't raise or return to main spack code.
+            # Just runs default exception handler and exits.
+            sys.excepthook(*sys.exc_info())
+            os._exit(1)
+
+    else:
+        # Parent process just waits for the child to complete.  If the
+        # child exited badly, assume it already printed an appropriate
+        # message.  Just make the parent exit with an error code.
+        pid, returncode = os.waitpid(pid, 0)
+        if returncode != 0:
+            sys.exit(1)
diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py
index 537db536dd..b96ac5af51 100644
--- a/lib/spack/spack/cmd/__init__.py
+++ b/lib/spack/spack/cmd/__init__.py
@@ -121,3 +121,18 @@ def elide_list(line_list, max_num=10):
         return line_list[:max_num-1] + ['...'] + line_list[-1:]
     else:
         return line_list
+
+
+def disambiguate_spec(spec):
+    matching_specs = spack.db.get_installed(spec)
+    if not matching_specs:
+        tty.die("Spec '%s' matches no installed packages." % spec)
+
+    elif len(matching_specs) > 1:
+        args =  ["%s matches multiple packages." % spec,
+                 "Matching packages:"]
+        args += ["  " + str(s) for s in matching_specs]
+        args += ["Use a more specific spec."]
+        tty.die(*args)
+
+    return matching_specs[0]
diff --git a/lib/spack/spack/cmd/activate.py b/lib/spack/spack/cmd/activate.py
new file mode 100644
index 0000000000..71eca4f453
--- /dev/null
+++ b/lib/spack/spack/cmd/activate.py
@@ -0,0 +1,56 @@
+##############################################################################
+# 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 external import argparse
+import llnl.util.tty as tty
+import spack
+import spack.cmd
+
+description = "Activate a package extension."
+
+def setup_parser(subparser):
+    subparser.add_argument(
+        '-f', '--force', action='store_true',
+        help="Activate without first activating dependencies.")
+    subparser.add_argument(
+        'spec', nargs=argparse.REMAINDER, help="spec of package extension to activate.")
+
+
+def activate(parser, args):
+    specs = spack.cmd.parse_specs(args.spec, concretize=True)
+    if len(specs) != 1:
+        tty.die("activate requires one spec.  %d given." % len(specs))
+
+    # TODO: remove this hack when DAG info is stored in dir layout.
+    # This ensures the ext spec is always normalized properly.
+    spack.db.get(specs[0])
+
+    spec = spack.cmd.disambiguate_spec(specs[0])
+    if not spec.package.is_extension:
+        tty.die("%s is not an extension." % spec.name)
+
+    if spec.package.activated:
+        tty.die("Package %s is already activated." % specs[0].short_spec)
+
+    spec.package.do_activate()
diff --git a/lib/spack/spack/cmd/clean.py b/lib/spack/spack/cmd/clean.py
index 79dd91c5bf..ec3b221988 100644
--- a/lib/spack/spack/cmd/clean.py
+++ b/lib/spack/spack/cmd/clean.py
@@ -23,6 +23,7 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from external import argparse
+import subprocess
 
 import llnl.util.tty as tty
 
diff --git a/lib/spack/spack/cmd/deactivate.py b/lib/spack/spack/cmd/deactivate.py
new file mode 100644
index 0000000000..bfec618c8e
--- /dev/null
+++ b/lib/spack/spack/cmd/deactivate.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 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 external import argparse
+import llnl.util.tty as tty
+
+import spack
+import spack.cmd
+from spack.graph import topological_sort
+
+description = "Deactivate a package extension."
+
+def setup_parser(subparser):
+    subparser.add_argument(
+        '-f', '--force', action='store_true',
+        help="Run deactivation even if spec is NOT currently activated.")
+    subparser.add_argument(
+        '-a', '--all', action='store_true',
+        help="Deactivate all extensions of an extendable pacakge, or "
+        "deactivate an extension AND its dependencies.")
+    subparser.add_argument(
+        'spec', nargs=argparse.REMAINDER, help="spec of package extension to deactivate.")
+
+
+def deactivate(parser, args):
+    specs = spack.cmd.parse_specs(args.spec, concretize=True)
+    if len(specs) != 1:
+        tty.die("deactivate requires one spec.  %d given." % len(specs))
+
+    # TODO: remove this hack when DAG info is stored properly.
+    # This ensures the ext spec is always normalized properly.
+    spack.db.get(specs[0])
+
+    spec = spack.cmd.disambiguate_spec(specs[0])
+    pkg = spec.package
+
+    if args.all:
+        if pkg.extendable:
+            tty.msg("Deactivating all extensions of %s" % pkg.spec.short_spec)
+            ext_pkgs = spack.db.installed_extensions_for(spec)
+            for ext_pkg in ext_pkgs:
+                ext_pkg.spec.normalize()
+                if ext_pkg.activated:
+                    ext_pkg.do_deactivate(force=True)
+
+        elif pkg.is_extension:
+            # TODO: store DAG info properly (see above)
+            spec.normalize()
+
+            tty.msg("Deactivating %s and all dependencies." % pkg.spec.short_spec)
+
+            topo_order = topological_sort(spec)
+            index = spec.index()
+
+            for name in topo_order:
+                espec = index[name]
+                epkg = espec.package
+
+                # TODO: store DAG info properly (see above)
+                epkg.spec.normalize()
+
+                if epkg.extends(pkg.extendee_spec):
+                    if epkg.activated or args.force:
+
+                        epkg.do_deactivate(force=args.force)
+
+        else:
+            tty.die("spack deactivate --all requires an extendable package or an extension.")
+
+    else:
+        if not pkg.is_extension:
+            tty.die("spack deactivate requires an extension.",
+                    "Did you mean 'spack deactivate --all'?")
+
+        if not args.force and not spec.package.activated:
+            tty.die("Package %s is not activated." % specs[0].short_spec)
+
+        spec.package.do_deactivate(force=args.force)
diff --git a/lib/spack/spack/cmd/extensions.py b/lib/spack/spack/cmd/extensions.py
new file mode 100644
index 0000000000..fc8e6842c3
--- /dev/null
+++ b/lib/spack/spack/cmd/extensions.py
@@ -0,0 +1,98 @@
+##############################################################################
+# 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 sys
+from external import argparse
+
+import llnl.util.tty as tty
+from llnl.util.tty.colify import colify
+
+import spack
+import spack.cmd
+import spack.cmd.find
+
+description = "List extensions for package."
+
+def setup_parser(subparser):
+    format_group = subparser.add_mutually_exclusive_group()
+    format_group.add_argument(
+        '-l', '--long', action='store_const', dest='mode', const='long',
+        help='Show dependency hashes as well as versions.')
+    format_group.add_argument(
+        '-p', '--paths', action='store_const', dest='mode', const='paths',
+        help='Show paths to extension install directories')
+    format_group.add_argument(
+        '-d', '--deps', action='store_const', dest='mode', const='deps',
+        help='Show full dependency DAG of extensions')
+
+    subparser.add_argument(
+        'spec', nargs=argparse.REMAINDER, help='Spec of package to list extensions for')
+
+
+def extensions(parser, args):
+    if not args.spec:
+        tty.die("extensions requires a package spec.")
+
+    # Checks
+    spec = spack.cmd.parse_specs(args.spec)
+    if len(spec) > 1:
+        tty.die("Can only list extensions for one package.")
+
+    if not spec[0].package.extendable:
+        tty.die("%s is not an extendable package." % spec[0].name)
+
+    spec = spack.cmd.disambiguate_spec(spec[0])
+
+    if not spec.package.extendable:
+        tty.die("%s does not have extensions." % spec.short_spec)
+
+    if not args.mode:
+        args.mode = 'short'
+
+    # List package names of extensions
+    extensions = spack.db.extensions_for(spec)
+    if not extensions:
+        tty.msg("%s has no extensions." % spec.cshort_spec)
+        return
+    tty.msg(spec.cshort_spec)
+    tty.msg("%d extensions:" % len(extensions))
+    colify(ext.name for ext in extensions)
+
+    # List specs of installed extensions.
+    installed  = [s.spec for s in spack.db.installed_extensions_for(spec)]
+    print
+    if not installed:
+        tty.msg("None installed.")
+        return
+    tty.msg("%d installed:" % len(installed))
+    spack.cmd.find.display_specs(installed, mode=args.mode)
+
+    # List specs of activated extensions.
+    activated = spack.install_layout.extension_map(spec)
+    print
+    if not activated:
+        tty.msg("None activated.")
+        return
+    tty.msg("%d currently activated:" % len(activated))
+    spack.cmd.find.display_specs(activated.values(), mode=args.mode)
diff --git a/lib/spack/spack/cmd/find.py b/lib/spack/spack/cmd/find.py
index 1de3413d42..70b10edb4e 100644
--- a/lib/spack/spack/cmd/find.py
+++ b/lib/spack/spack/cmd/find.py
@@ -41,13 +41,13 @@ description ="Find installed spack packages"
 def setup_parser(subparser):
     format_group = subparser.add_mutually_exclusive_group()
     format_group.add_argument(
-        '-l', '--long', action='store_true', dest='long',
+        '-l', '--long', action='store_const', dest='mode', const='long',
         help='Show dependency hashes as well as versions.')
     format_group.add_argument(
-        '-p', '--paths', action='store_true', dest='paths',
+        '-p', '--paths', action='store_const', dest='mode', const='paths',
         help='Show paths to package install directories')
     format_group.add_argument(
-        '-d', '--deps', action='store_true', dest='full_deps',
+        '-d', '--deps', action='store_const', dest='mode', const='deps',
         help='Show full dependency DAG of installed packages')
 
     subparser.add_argument(
@@ -55,26 +55,8 @@ def setup_parser(subparser):
         help='optional specs to filter results')
 
 
-def find(parser, args):
-    # Filter out specs that don't exist.
-    query_specs = spack.cmd.parse_specs(args.query_specs)
-    query_specs, nonexisting = partition_list(
-        query_specs, lambda s: spack.db.exists(s.name))
-
-    if nonexisting:
-        msg = "No such package%s: " % ('s' if len(nonexisting) > 1 else '')
-        msg += ", ".join(s.name for s in nonexisting)
-        tty.msg(msg)
-
-        if not query_specs:
-            return
-
-    # Get all the specs the user asked for
-    if not query_specs:
-        specs = set(spack.db.installed_package_specs())
-    else:
-        results = [set(spack.db.get_installed(qs)) for qs in query_specs]
-        specs = set.union(*results)
+def display_specs(specs, **kwargs):
+    mode = kwargs.get('mode', 'short')
 
     # Make a dict with specs keyed by architecture and compiler.
     index = index_by(specs, ('architecture', 'compiler'))
@@ -92,7 +74,7 @@ def find(parser, args):
         specs.sort()
 
         abbreviated = [s.format('$_$@$+', color=True) for s in specs]
-        if args.paths:
+        if mode == 'paths':
             # Print one spec per line along with prefix path
             width = max(len(s) for s in abbreviated)
             width += 2
@@ -101,11 +83,47 @@ def find(parser, args):
             for abbrv, spec in zip(abbreviated, specs):
                 print format % (abbrv, spec.prefix)
 
-        elif args.full_deps:
+        elif mode == 'deps':
             for spec in specs:
-                print spec.tree(indent=4, format='$_$@$+', color=True),
-        else:
+                print spec.tree(indent=4, format='$_$@$+$#', color=True),
+
+        elif mode in ('short', 'long'):
             fmt = '$-_$@$+'
-            if args.long:
+            if mode == 'long':
                 fmt += '$#'
             colify(s.format(fmt, color=True) for s in specs)
+
+        else:
+            raise ValueError(
+                "Invalid mode for display_specs: %s. Must be one of (paths, deps, short)." % mode)
+
+
+
+def find(parser, args):
+    # Filter out specs that don't exist.
+    query_specs = spack.cmd.parse_specs(args.query_specs)
+    query_specs, nonexisting = partition_list(
+        query_specs, lambda s: spack.db.exists(s.name))
+
+    if nonexisting:
+        msg = "No such package%s: " % ('s' if len(nonexisting) > 1 else '')
+        msg += ", ".join(s.name for s in nonexisting)
+        tty.msg(msg)
+
+        if not query_specs:
+            return
+
+    # Get all the specs the user asked for
+    if not query_specs:
+        specs = set(spack.db.installed_package_specs())
+    else:
+        results = [set(spack.db.get_installed(qs)) for qs in query_specs]
+        specs = set.union(*results)
+
+    if not args.mode:
+        args.mode = 'short'
+
+    if sys.stdout.isatty():
+        tty.msg("%d installed packages." % len(specs))
+    display_specs(specs, mode=args.mode)
+
diff --git a/lib/spack/spack/cmd/location.py b/lib/spack/spack/cmd/location.py
index 509c336b69..810c34d0a6 100644
--- a/lib/spack/spack/cmd/location.py
+++ b/lib/spack/spack/cmd/location.py
@@ -77,37 +77,30 @@ def location(parser, args):
             tty.die("You must supply a spec.")
         if len(specs) != 1:
             tty.die("Too many specs.  Supply only one.")
-        spec = specs[0]
 
         if args.install_dir:
             # install_dir command matches against installed specs.
-            matching_specs = spack.db.get_installed(spec)
-            if not matching_specs:
-                tty.die("Spec '%s' matches no installed packages." % spec)
+            spec = spack.cmd.disambiguate_spec(specs[0])
+            print spec.prefix
 
-            elif len(matching_specs) > 1:
-                args =  ["%s matches multiple packages." % spec,
-                         "Matching packages:"]
-                args += ["  " + str(s) for s in matching_specs]
-                args += ["Use a more specific spec."]
-                tty.die(*args)
+        else:
+            spec = specs[0]
 
-            print matching_specs[0].prefix
+            if args.package_dir:
+                # This one just needs the spec name.
+                print join_path(spack.db.root, spec.name)
 
-        elif args.package_dir:
-            # This one just needs the spec name.
-            print join_path(spack.db.root, spec.name)
+            else:
+                # These versions need concretized specs.
+                spec.concretize()
+                pkg = spack.db.get(spec)
+
+                if args.stage_dir:
+                    print pkg.stage.path
+
+                else:  #  args.build_dir is the default.
+                    if not pkg.stage.source_path:
+                        tty.die("Build directory does not exist yet. Run this to create it:",
+                                "spack stage " + " ".join(args.spec))
+                    print pkg.stage.source_path
 
-        else:
-            # These versions need concretized specs.
-            spec.concretize()
-            pkg = spack.db.get(spec)
-
-            if args.stage_dir:
-                print pkg.stage.path
-
-            else:  #  args.build_dir is the default.
-                if not pkg.stage.source_path:
-                    tty.die("Build directory does not exist yet. Run this to create it:",
-                            "spack stage " + " ".join(args.spec))
-                print pkg.stage.source_path
diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index e787c460ad..0962942f43 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -65,7 +65,6 @@ def uninstall(parser, args):
                      "  b) use a more specific spec."]
             tty.die(*args)
 
-
         if len(matching_specs) == 0:
             tty.die("%s does not match any installed packages." % spec)
 
diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index 42cac0c9d2..b2cf5dc801 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -27,9 +27,11 @@ import os
 import exceptions
 import hashlib
 import shutil
+import tempfile
 from contextlib import closing
 
 import llnl.util.tty as tty
+from llnl.util.lang import memoized
 from llnl.util.filesystem import join_path, mkdirp
 
 import spack
@@ -53,6 +55,19 @@ class DirectoryLayout(object):
         self.root = root
 
 
+    @property
+    def hidden_file_paths(self):
+        """Return a list of hidden files used by the directory layout.
+
+        Paths are relative to the root of an install directory.
+
+        If the directory layout uses no hidden files to maintain
+        state, this should return an empty container, e.g. [] or (,).
+
+        """
+        raise NotImplementedError()
+
+
     def all_specs(self):
         """To be implemented by subclasses to traverse all specs for which there is
            a directory within the root.
@@ -71,6 +86,42 @@ class DirectoryLayout(object):
         raise NotImplementedError()
 
 
+    def extension_map(self, spec):
+        """Get a dict of currently installed extension packages for a spec.
+
+           Dict maps { name : extension_spec }
+           Modifying dict does not affect internals of this layout.
+        """
+        raise NotImplementedError()
+
+
+    def check_extension_conflict(self, spec, ext_spec):
+        """Ensure that ext_spec can be activated in spec.
+
+           If not, raise ExtensionAlreadyInstalledError or
+           ExtensionConflictError.
+        """
+        raise NotImplementedError()
+
+
+    def check_activated(self, spec, ext_spec):
+        """Ensure that ext_spec can be removed from spec.
+
+           If not, raise NoSuchExtensionError.
+        """
+        raise NotImplementedError()
+
+
+    def add_extension(self, spec, ext_spec):
+        """Add to the list of currently installed extensions."""
+        raise NotImplementedError()
+
+
+    def remove_extension(self, spec, ext_spec):
+        """Remove from the list of currently installed extensions."""
+        raise NotImplementedError()
+
+
     def path_for_spec(self, spec):
         """Return an absolute path from the root to a directory for the spec."""
         _check_concrete(spec)
@@ -81,12 +132,17 @@ class DirectoryLayout(object):
 
 
     def remove_path_for_spec(self, spec):
-        """Removes a prefix and any empty parent directories from the root."""
+        """Removes a prefix and any empty parent directories from the root.
+           Raised RemoveFailedError if something goes wrong.
+        """
         path = self.path_for_spec(spec)
         assert(path.startswith(self.root))
 
         if os.path.exists(path):
-            shutil.rmtree(path, True)
+            try:
+                shutil.rmtree(path)
+            except exceptions.OSError, e:
+                raise RemoveFailedError(spec, path, e)
 
         path = os.path.dirname(path)
         while path != self.root:
@@ -134,9 +190,18 @@ class SpecHashDirectoryLayout(DirectoryLayout):
         """Prefix size is number of characters in the SHA-1 prefix to use
            to make each hash unique.
         """
-        spec_file_name   = kwargs.get('spec_file_name', '.spec')
+        spec_file_name = kwargs.get('spec_file_name', '.spec')
+        extension_file_name = kwargs.get('extension_file_name', '.extensions')
         super(SpecHashDirectoryLayout, self).__init__(root)
         self.spec_file_name = spec_file_name
+        self.extension_file_name = extension_file_name
+
+        # Cache of already written/read extension maps.
+        self._extension_maps = {}
+
+    @property
+    def hidden_file_paths(self):
+        return ('.spec', '.extensions')
 
 
     def relative_path_for_spec(self, spec):
@@ -159,6 +224,9 @@ class SpecHashDirectoryLayout(DirectoryLayout):
 
         if all(spack.db.exists(s.name) for s in spec.traverse()):
             copy = spec.copy()
+
+            # TODO: It takes a lot of time to normalize every spec on read.
+            # TODO: Storing graph info with spec files would fix this.
             copy.normalize()
             if copy.concrete:
                 return copy   # These are specs spack still understands.
@@ -212,17 +280,116 @@ class SpecHashDirectoryLayout(DirectoryLayout):
         self.write_spec(spec, spec_file_path)
 
 
+    @memoized
     def all_specs(self):
         if not os.path.isdir(self.root):
-            return
+            return []
 
+        specs = []
         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_name)
             if os.path.exists(spec_file_path):
                 spec = self.read_spec(spec_file_path)
-                yield spec
+                specs.append(spec)
+        return specs
+
+
+    def extension_file_path(self, spec):
+        """Gets full path to an installed package's extension file"""
+        _check_concrete(spec)
+        return join_path(self.path_for_spec(spec), self.extension_file_name)
+
+
+    def _extension_map(self, spec):
+        """Get a dict<name -> spec> for all extensions currnetly
+           installed for this package."""
+        _check_concrete(spec)
+
+        if not spec in self._extension_maps:
+            path = self.extension_file_path(spec)
+            if not os.path.exists(path):
+                self._extension_maps[spec] = {}
+
+            else:
+                exts = {}
+                with closing(open(path)) as ext_file:
+                    for line in ext_file:
+                        try:
+                            spec = Spec(line.strip())
+                            exts[spec.name] = spec
+                        except spack.error.SpackError, e:
+                            # TODO: do something better here -- should be
+                            # resilient to corrupt files.
+                            raise InvalidExtensionSpecError(str(e))
+                self._extension_maps[spec] = exts
+
+        return self._extension_maps[spec]
+
+
+    def extension_map(self, spec):
+        """Defensive copying version of _extension_map() for external API."""
+        return self._extension_map(spec).copy()
+
+
+    def check_extension_conflict(self, spec, ext_spec):
+        exts = self._extension_map(spec)
+        if ext_spec.name in exts:
+            installed_spec = exts[ext_spec.name]
+            if ext_spec == installed_spec:
+                raise ExtensionAlreadyInstalledError(spec, ext_spec)
+            else:
+                raise ExtensionConflictError(spec, ext_spec, installed_spec)
+
+
+    def check_activated(self, spec, ext_spec):
+        exts = self._extension_map(spec)
+        if (not ext_spec.name in exts) or (ext_spec != exts[ext_spec.name]):
+            raise NoSuchExtensionError(spec, ext_spec)
+
+
+    def _write_extensions(self, spec, extensions):
+        path = self.extension_file_path(spec)
+
+        # Create a temp file in the same directory as the actual file.
+        dirname, basename = os.path.split(path)
+        tmp = tempfile.NamedTemporaryFile(
+            prefix=basename, dir=dirname, delete=False)
+
+        # Write temp file.
+        with closing(tmp):
+            for extension in sorted(extensions.values()):
+                tmp.write("%s\n" % extension)
+
+        # Atomic update by moving tmpfile on top of old one.
+        os.rename(tmp.name, path)
+
+
+    def add_extension(self, spec, ext_spec):
+        _check_concrete(spec)
+        _check_concrete(ext_spec)
+
+        # Check whether it's already installed or if it's a conflict.
+        exts = self._extension_map(spec)
+        self.check_extension_conflict(spec, ext_spec)
+
+        # do the actual adding.
+        exts[ext_spec.name] = ext_spec
+        self._write_extensions(spec, exts)
+
+
+    def remove_extension(self, spec, ext_spec):
+        _check_concrete(spec)
+        _check_concrete(ext_spec)
+
+        # Make sure it's installed before removing.
+        exts = self._extension_map(spec)
+        self.check_activated(spec, ext_spec)
+
+        # do the actual removing.
+        del exts[ext_spec.name]
+        self._write_extensions(spec, exts)
 
 
 class DirectoryLayoutError(SpackError):
@@ -239,6 +406,15 @@ class SpecHashCollisionError(DirectoryLayoutError):
             % installed_spec, new_spec)
 
 
+class RemoveFailedError(DirectoryLayoutError):
+    """Raised when a DirectoryLayout cannot remove an install prefix."""
+    def __init__(self, installed_spec, prefix, error):
+        super(RemoveFailedError, self).__init__(
+            'Could not remove prefix %s for %s : %s'
+            % prefix, installed_spec.short_spec, error)
+        self.cause = error
+
+
 class InconsistentInstallDirectoryError(DirectoryLayoutError):
     """Raised when a package seems to be installed to the wrong place."""
     def __init__(self, message):
@@ -250,3 +426,34 @@ class InstallDirectoryAlreadyExistsError(DirectoryLayoutError):
     def __init__(self, path):
         super(InstallDirectoryAlreadyExistsError, self).__init__(
             "Install path %s already exists!")
+
+
+class InvalidExtensionSpecError(DirectoryLayoutError):
+    """Raised when an extension file has a bad spec in it."""
+    def __init__(self, message):
+        super(InvalidExtensionSpecError, self).__init__(message)
+
+
+class ExtensionAlreadyInstalledError(DirectoryLayoutError):
+    """Raised when an extension is added to a package that already has it."""
+    def __init__(self, spec, ext_spec):
+        super(ExtensionAlreadyInstalledError, self).__init__(
+            "%s is already installed in %s" % (ext_spec.short_spec, spec.short_spec))
+
+
+class ExtensionConflictError(DirectoryLayoutError):
+    """Raised when an extension is added to a package that already has it."""
+    def __init__(self, spec, ext_spec, conflict):
+        super(ExtensionConflictError, self).__init__(
+            "%s cannot be installed in %s because it conflicts with %s."% (
+                ext_spec.short_spec, spec.short_spec, conflict.short_spec))
+
+
+class NoSuchExtensionError(DirectoryLayoutError):
+    """Raised when an extension isn't there on deactivate."""
+    def __init__(self, spec, ext_spec):
+        super(NoSuchExtensionError, self).__init__(
+            "%s cannot be removed from %s because it's not activated."% (
+                ext_spec.short_spec, spec.short_spec))
+
+
diff --git a/lib/spack/spack/hooks/__init__.py b/lib/spack/spack/hooks/__init__.py
index 98b7f2323f..1c44e8abaa 100644
--- a/lib/spack/spack/hooks/__init__.py
+++ b/lib/spack/spack/hooks/__init__.py
@@ -31,7 +31,9 @@
 
    Currently the following hooks are supported:
 
+      * pre_install()
       * post_install()
+      * pre_uninstall()
       * post_uninstall()
 
    This can be used to implement support for things like module
@@ -70,5 +72,8 @@ class HookRunner(object):
 #
 # Define some functions that can be called to fire off hooks.
 #
-post_install = HookRunner('post_install')
+pre_install    = HookRunner('pre_install')
+post_install   = HookRunner('post_install')
+
+pre_uninstall  = HookRunner('pre_uninstall')
 post_uninstall = HookRunner('post_uninstall')
diff --git a/lib/spack/spack/hooks/extensions.py b/lib/spack/spack/hooks/extensions.py
new file mode 100644
index 0000000000..cf87a78c8c
--- /dev/null
+++ b/lib/spack/spack/hooks/extensions.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
+##############################################################################
+
+import spack
+
+
+def pre_uninstall(pkg):
+    # Need to do this b/c uninstall does not automatically do it.
+    # TODO: store full graph info in stored .spec file.
+    pkg.spec.normalize()
+
+    if pkg.is_extension:
+        if pkg.activated:
+            pkg.do_deactivate(force=True)
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 755e9ea900..7d2ca97a62 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -49,6 +49,7 @@ import os
 import re
 import textwrap
 import shutil
+from glob import glob
 from contextlib import closing
 
 import llnl.util.tty as tty
@@ -123,6 +124,13 @@ class EnvModule(object):
                 if os.path.isdir(directory):
                     add_path(var, directory)
 
+            # Add python path unless it's an actual python installation
+            # TODO: is there a better way to do this?
+            if self.spec.name != 'python':
+                site_packages = glob(join_path(self.spec.prefix.lib, "python*/site-packages"))
+                if site_packages:
+                    add_path('PYTHONPATH', site_packages[0])
+
             # short description is just the package + version
             # TODO: maybe packages can optionally provide it.
             self.short_description = self.spec.format("$_ $@")
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 1dfd3d1c83..bc8541a184 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -45,6 +45,7 @@ import textwrap
 from StringIO import StringIO
 
 import llnl.util.tty as tty
+from llnl.util.link_tree import LinkTree
 from llnl.util.filesystem import *
 from llnl.util.lang import *
 
@@ -320,12 +321,21 @@ class Package(object):
     """Patches to apply to newly expanded source, if any."""
     patches = {}
 
+    """Specs of package this one extends, or None.
+
+    Currently, ppackages can extend at most one other package.
+    """
+    extendees = {}
+
     #
     # These are default values for instance variables.
     #
     """By default we build in parallel.  Subclasses can override this."""
     parallel = True
 
+    """Most packages are NOT extendable.  Set to True if you want extensions."""
+    extendable = False
+
 
     def __init__(self, spec):
         # this determines how the package should be built.
@@ -395,6 +405,9 @@ class Package(object):
         self._fetch_time = 0.0
         self._total_time = 0.0
 
+        if self.is_extension:
+            spack.db.get(self.extendee_spec)._check_extendable()
+
 
     @property
     def version(self):
@@ -481,6 +494,47 @@ class Package(object):
         self._fetcher = f
 
 
+    @property
+    def extendee_spec(self):
+        """Spec of the extendee of this package, or None if it is not an extension."""
+        if not self.extendees:
+            return None
+        name = next(iter(self.extendees))
+        if not name in self.spec:
+            spec, kwargs = self.extendees[name]
+            return spec
+
+        # Need to do this to get the concrete version of the spec
+        return self.spec[name]
+
+
+    @property
+    def extendee_args(self):
+        """Spec of the extendee of this package, or None if it is not an extension."""
+        if not self.extendees:
+            return None
+        name = next(iter(self.extendees))
+        return self.extendees[name][1]
+
+
+    @property
+    def is_extension(self):
+        return len(self.extendees) > 0
+
+
+    def extends(self, spec):
+        return (spec.name in self.extendees and
+                spec.satisfies(self.extendees[spec.name][0]))
+
+
+    @property
+    def activated(self):
+        if not self.is_extension:
+            raise ValueError("is_extension called on package that is not an extension.")
+        exts = spack.install_layout.extension_map(self.extendee_spec)
+        return (self.name in exts) and (exts[self.name] == self.spec)
+
+
     def preorder_traversal(self, visited=None, **kwargs):
         """This does a preorder traversal of the package's dependence DAG."""
         virtual = kwargs.get("virtual", False)
@@ -741,34 +795,27 @@ class Package(object):
         tty.msg("Installing %s" % self.name)
 
         if not ignore_deps:
-            self.do_install_dependencies()
+            self.do_install_dependencies(**kwargs)
 
         start_time = time.time()
         if not fake_install:
             self.do_patch()
 
-        # Fork a child process to do the build.  This allows each
-        # package authors to have full control over their environment,
-        # etc. without offecting other builds that might be executed
-        # in the same spack call.
-        try:
-            pid = os.fork()
-        except OSError, e:
-            raise InstallError("Unable to fork build process: %s" % e)
+        # create the install directory.  The install layout
+        # handles this in case so that it can use whatever
+        # package naming scheme it likes.
+        spack.install_layout.make_path_for_spec(self.spec)
 
-        if pid == 0:
+        def real_work():
             try:
                 tty.msg("Building %s." % self.name)
 
-                # create the install directory.  The install layout
-                # handles this in case so that it can use whatever
-                # package naming scheme it likes.
-                spack.install_layout.make_path_for_spec(self.spec)
+                # Run the pre-install hook in the child process after
+                # the directory is created.
+                spack.hooks.pre_install(self)
 
                 # Set up process's build environment before running install.
                 self.stage.chdir_to_source()
-                build_env.setup_package(self)
-
                 if fake_install:
                     self.do_fake_install()
                 else:
@@ -776,10 +823,7 @@ class Package(object):
                     self.install(self.spec, self.prefix)
 
                 # Ensure that something was actually installed.
-                if not os.listdir(self.prefix):
-                    raise InstallError(
-                        "Install failed for %s.  Nothing was installed!"
-                        % self.name)
+                self._sanity_check_install()
 
                 # On successful install, remove the stage.
                 if not keep_stage:
@@ -790,14 +834,10 @@ class Package(object):
                 build_time = self._total_time - self._fetch_time
 
                 tty.msg("Successfully installed %s." % self.name,
-                        "Fetch: %.2f sec.  Build: %.2f sec.  Total: %.2f sec."
-                        % (self._fetch_time, build_time, self._total_time))
+                        "Fetch: %s.  Build: %s.  Total: %s."
+                        % (_hms(self._fetch_time), _hms(build_time), _hms(self._total_time)))
                 print_pkg(self.prefix)
 
-                # Use os._exit here to avoid raising a SystemExit exception,
-                # which interferes with unit tests.
-                os._exit(0)
-
             except:
                 if not keep_prefix:
                     # If anything goes wrong, remove the install prefix
@@ -807,28 +847,26 @@ class Package(object):
                              "Spack will think this package is installed." +
                              "Manually remove this directory to fix:",
                              self.prefix)
+                raise
 
-                # Child doesn't raise or return to main spack code.
-                # Just runs default exception handler and exits.
-                sys.excepthook(*sys.exc_info())
-                os._exit(1)
-
-        # Parent process just waits for the child to complete.  If the
-        # child exited badly, assume it already printed an appropriate
-        # message.  Just make the parent exit with an error code.
-        pid, returncode = os.waitpid(pid, 0)
-        if returncode != 0:
-            sys.exit(1)
-
+        build_env.fork(self, real_work)
 
         # Once everything else is done, run post install hooks
         spack.hooks.post_install(self)
 
 
-    def do_install_dependencies(self):
+    def _sanity_check_install(self):
+        installed = set(os.listdir(self.prefix))
+        installed.difference_update(spack.install_layout.hidden_file_paths)
+        if not installed:
+            raise InstallError(
+                "Install failed for %s.  Nothing was installed!" % self.name)
+
+
+    def do_install_dependencies(self, **kwargs):
         # Pass along paths of dependencies here
         for dep in self.spec.dependencies.values():
-            dep.package.do_install()
+            dep.package.do_install(**kwargs)
 
 
     @property
@@ -840,6 +878,32 @@ class Package(object):
                           fromlist=[self.__class__.__name__])
 
 
+    def setup_dependent_environment(self, module, spec, dependent_spec):
+        """Called before the install() method of dependents.
+
+        Default implementation does nothing, but this can be
+        overridden by an extendable package to set up the install
+        environment for its extensions.  This is useful if there are
+        some common steps to installing all extensions for a
+        certain package.
+
+        Some examples:
+
+        1. Installing python modules generally requires PYTHONPATH to
+           point to the lib/pythonX.Y/site-packages directory in the
+           module's install prefix.  This could set that variable.
+
+        2. Extensions often need to invoke the 'python' interpreter
+           from the Python installation being extended.  This routine can
+           put a 'python' Execuable object in the module scope for the
+           extension package to simplify extension installs.
+
+        3. A lot of Qt extensions need QTDIR set.  This can be used to do that.
+
+        """
+        pass
+
+
     def install(self, spec, prefix):
         """Package implementations override this with their own build configuration."""
         raise InstallError("Package %s provides no install method!" % self.name)
@@ -859,6 +923,10 @@ class Package(object):
                 "The following installed packages depend on it: %s" %
                 ' '.join(formatted_deps))
 
+        # Pre-uninstall hook runs first.
+        spack.hooks.pre_uninstall(self)
+
+        # Uninstalling in Spack only requires removing the prefix.
         self.remove_prefix()
         tty.msg("Successfully uninstalled %s." % self.spec.short_spec)
 
@@ -866,6 +934,119 @@ class Package(object):
         spack.hooks.post_uninstall(self)
 
 
+    def _check_extendable(self):
+        if not self.extendable:
+            raise ValueError("Package %s is not extendable!" % self.name)
+
+
+    def _sanity_check_extension(self):
+        if not self.is_extension:
+            raise ValueError("This package is not an extension.")
+        extendee_package = self.extendee_spec.package
+        extendee_package._check_extendable()
+
+        if not extendee_package.installed:
+            raise ValueError("Can only (de)activate extensions for installed packages.")
+        if not self.installed:
+            raise ValueError("Extensions must first be installed.")
+        if not self.extendee_spec.name in self.extendees:
+            raise ValueError("%s does not extend %s!" % (self.name, self.extendee.name))
+
+
+    def do_activate(self, **kwargs):
+        """Called on an etension to invoke the extendee's activate method.
+
+        Commands should call this routine, and should not call
+        activate() directly.
+        """
+        self._sanity_check_extension()
+        force = kwargs.get('force', False)
+
+        # TODO: get rid of this normalize - DAG handling.
+        self.spec.normalize()
+
+        spack.install_layout.check_extension_conflict(self.extendee_spec, self.spec)
+
+        if not force:
+            for spec in self.spec.traverse(root=False):
+                if spec.package.extends(self.extendee_spec):
+                    # TODO: fix this normalize() requirement -- revisit DAG handling.
+                    spec.package.spec.normalize()
+                    if not spec.package.activated:
+                        spec.package.do_activate(**kwargs)
+
+        self.extendee_spec.package.activate(self, **self.extendee_args)
+
+        spack.install_layout.add_extension(self.extendee_spec, self.spec)
+        tty.msg("Activated extension %s for %s."
+                % (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
+
+
+    def activate(self, extension, **kwargs):
+        """Symlinks all files from the extension into extendee's install dir.
+
+        Package authors can override this method to support other
+        extension mechanisms.  Spack internals (commands, hooks, etc.)
+        should call do_activate() method so that proper checks are
+        always executed.
+
+        """
+        def ignore(filename):
+            return (filename in spack.install_layout.hidden_file_paths or
+                    kwargs.get('ignore', lambda f: False)(filename))
+
+        tree = LinkTree(extension.prefix)
+        conflict = tree.find_conflict(self.prefix, ignore=ignore)
+        if conflict:
+            raise ExtensionConflictError(conflict)
+        tree.merge(self.prefix, ignore=ignore)
+
+
+    def do_deactivate(self, **kwargs):
+        """Called on the extension to invoke extendee's deactivate() method."""
+        self._sanity_check_extension()
+        force = kwargs.get('force', False)
+
+        # Allow a force deactivate to happen.  This can unlink
+        # spurious files if something was corrupted.
+        if not force:
+            spack.install_layout.check_activated(self.extendee_spec, self.spec)
+
+            activated = spack.install_layout.extension_map(self.extendee_spec)
+            for name, aspec in activated.items():
+                if aspec != self.spec and self.spec in aspec:
+                    raise ActivationError(
+                        "Cannot deactivate %s beacuse %s is activated and depends on it."
+                        % (self.spec.short_spec, aspec.short_spec))
+
+        self.extendee_spec.package.deactivate(self, **self.extendee_args)
+
+        # redundant activation check -- makes SURE the spec is not
+        # still activated even if something was wrong above.
+        if self.activated:
+            spack.install_layout.remove_extension(self.extendee_spec, self.spec)
+
+        tty.msg("Deactivated extension %s for %s."
+                % (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
+
+
+    def deactivate(self, extension, **kwargs):
+        """Unlinks all files from extension out of this package's install dir.
+
+        Package authors can override this method to support other
+        extension mechanisms.  Spack internals (commands, hooks, etc.)
+        should call do_deactivate() method so that proper checks are
+        always executed.
+
+        """
+        def ignore(filename):
+            return (filename in spack.install_layout.hidden_file_paths or
+                    kwargs.get('ignore', lambda f: False)(filename))
+
+        tree = LinkTree(extension.prefix)
+        tree.unmerge(self.prefix, ignore=ignore)
+
+
     def do_clean(self):
         if self.stage.expanded_archive_path:
             self.stage.chdir_to_source()
@@ -1011,6 +1192,18 @@ def print_pkg(message):
     print message
 
 
+def _hms(seconds):
+    """Convert time in seconds to hours, minutes, seconds."""
+    m, s = divmod(seconds, 60)
+    h, m = divmod(m, 60)
+
+    parts = []
+    if h: parts.append("%dh" % h)
+    if m: parts.append("%dm" % m)
+    if s: parts.append("%.2fs" % s)
+    return ' '.join(parts)
+
+
 class FetchError(spack.error.SpackError):
     """Raised when something goes wrong during fetch."""
     def __init__(self, message, long_msg=None):
@@ -1057,3 +1250,17 @@ class NoURLError(PackageError):
     def __init__(self, cls):
         super(NoURLError, self).__init__(
             "Package %s has no version with a URL." % cls.__name__)
+
+
+class ExtensionError(PackageError): pass
+
+
+class ExtensionConflictError(ExtensionError):
+    def __init__(self, path):
+        super(ExtensionConflictError, self).__init__(
+            "Extension blocked by file: %s" % path)
+
+
+class ActivationError(ExtensionError):
+    def __init__(self, msg, long_msg=None):
+        super(ActivationError, self).__init__(msg, long_msg)
diff --git a/lib/spack/spack/packages.py b/lib/spack/spack/packages.py
index db43d3909a..43c4c191c1 100644
--- a/lib/spack/spack/packages.py
+++ b/lib/spack/spack/packages.py
@@ -77,6 +77,8 @@ class PackageDB(object):
                 copy = spec.copy()
                 self.instances[copy] = package_class(copy)
             except Exception, e:
+                if spack.debug:
+                    sys.excepthook(*sys.exc_info())
                 raise FailedConstructorError(spec.name, e)
 
         return self.instances[spec]
@@ -110,6 +112,24 @@ class PackageDB(object):
         return providers
 
 
+    @_autospec
+    def extensions_for(self, extendee_spec):
+        return [p for p in self.all_packages() if p.extends(extendee_spec)]
+
+
+    @_autospec
+    def installed_extensions_for(self, extendee_spec):
+        for s in self.installed_package_specs():
+            try:
+                if s.package.extends(extendee_spec):
+                    yield s.package
+            except UnknownPackageError, e:
+                # Skip packages we know nothing about
+                continue
+                # TODO: add some conditional way to do this instead of
+                # catching exceptions.
+
+
     def dirname_for_package_name(self, pkg_name):
         """Get the directory name for a particular package.  This is the
            directory that contains its package.py file."""
@@ -172,6 +192,7 @@ class PackageDB(object):
             yield self.get(name)
 
 
+    @memoized
     def exists(self, pkg_name):
         """Whether a package with the supplied name exists ."""
         return os.path.exists(self.filename_for_package_name(pkg_name))
diff --git a/lib/spack/spack/relations.py b/lib/spack/spack/relations.py
index b1f4348945..a0c7723473 100644
--- a/lib/spack/spack/relations.py
+++ b/lib/spack/spack/relations.py
@@ -68,7 +68,7 @@ provides
         spack install mpileaks ^mvapich
         spack install mpileaks ^mpich
 """
-__all__ = [ 'depends_on', 'provides', 'patch', 'version' ]
+__all__ = [ 'depends_on', 'extends', 'provides', 'patch', 'version' ]
 
 import re
 import inspect
@@ -107,8 +107,9 @@ def depends_on(*specs):
     """Adds a dependencies local variable in the locals of
        the calling class, based on args. """
     pkg = get_calling_package_name()
+    clocals = caller_locals()
+    dependencies = clocals.setdefault('dependencies', {})
 
-    dependencies = caller_locals().setdefault('dependencies', {})
     for string in specs:
         for spec in spack.spec.parse(string):
             if pkg == spec.name:
@@ -116,6 +117,34 @@ def depends_on(*specs):
             dependencies[spec.name] = spec
 
 
+def extends(spec, **kwargs):
+    """Same as depends_on, but dependency is symlinked into parent prefix.
+
+    This is for Python and other language modules where the module
+    needs to be installed into the prefix of the Python installation.
+    Spack handles this by installing modules into their own prefix,
+    but allowing ONE module version to be symlinked into a parent
+    Python install at a time.
+
+    keyword arguments can be passed to extends() so that extension
+    packages can pass parameters to the extendee's extension
+    mechanism.
+
+    """
+    pkg = get_calling_package_name()
+    clocals = caller_locals()
+    dependencies = clocals.setdefault('dependencies', {})
+    extendees = clocals.setdefault('extendees', {})
+    if extendees:
+        raise RelationError("Packages can extend at most one other package.")
+
+    spec = Spec(spec)
+    if pkg == spec.name:
+        raise CircularReferenceError('extends', pkg)
+    dependencies[spec.name] = spec
+    extendees[spec.name] = (spec, kwargs)
+
+
 def provides(*specs, **kwargs):
     """Allows packages to provide a virtual dependency.  If a package provides
        'mpi', other packages can declare that they depend on "mpi", and spack
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index 2f4fe9ca24..dffdccaddb 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -553,6 +553,13 @@ class Spec(object):
 
 
     @property
+    def cshort_spec(self):
+        """Returns a version of the spec with the dependencies hashed
+           instead of completely enumerated."""
+        return self.format('$_$@$%@$+$=$#', color=True)
+
+
+    @property
     def prefix(self):
         return Prefix(spack.install_layout.path_for_spec(self))
 
diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py
index 0eda667abc..c53e6774fc 100644
--- a/lib/spack/spack/test/__init__.py
+++ b/lib/spack/spack/test/__init__.py
@@ -51,7 +51,8 @@ test_names = ['versions',
               'hg_fetch',
               'mirror',
               'url_extrapolate',
-              'cc']
+              'cc',
+              'link_tree']
 
 
 def list_tests():
diff --git a/lib/spack/spack/test/link_tree.py b/lib/spack/spack/test/link_tree.py
new file mode 100644
index 0000000000..bc7c2c6b5e
--- /dev/null
+++ b/lib/spack/spack/test/link_tree.py
@@ -0,0 +1,153 @@
+##############################################################################
+# 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
+import unittest
+import shutil
+import tempfile
+from contextlib import closing
+
+from llnl.util.filesystem import *
+from llnl.util.link_tree import LinkTree
+
+from spack.stage import Stage
+
+
+class LinkTreeTest(unittest.TestCase):
+    """Tests Spack's LinkTree class."""
+
+    def setUp(self):
+        self.stage = Stage('link-tree-test')
+
+        with working_dir(self.stage.path):
+            touchp('source/1')
+            touchp('source/a/b/2')
+            touchp('source/a/b/3')
+            touchp('source/c/4')
+            touchp('source/c/d/5')
+            touchp('source/c/d/6')
+            touchp('source/c/d/e/7')
+
+        source_path = os.path.join(self.stage.path, 'source')
+        self.link_tree = LinkTree(source_path)
+
+
+    def tearDown(self):
+        if self.stage:
+            self.stage.destroy()
+
+
+    def check_file_link(self, filename):
+        self.assertTrue(os.path.isfile(filename))
+        self.assertTrue(os.path.islink(filename))
+
+
+    def check_dir(self, filename):
+        self.assertTrue(os.path.isdir(filename))
+
+
+    def test_merge_to_new_directory(self):
+        with working_dir(self.stage.path):
+            self.link_tree.merge('dest')
+
+            self.check_file_link('dest/1')
+            self.check_file_link('dest/a/b/2')
+            self.check_file_link('dest/a/b/3')
+            self.check_file_link('dest/c/4')
+            self.check_file_link('dest/c/d/5')
+            self.check_file_link('dest/c/d/6')
+            self.check_file_link('dest/c/d/e/7')
+
+            self.link_tree.unmerge('dest')
+
+            self.assertFalse(os.path.exists('dest'))
+
+
+    def test_merge_to_existing_directory(self):
+        with working_dir(self.stage.path):
+
+            touchp('dest/x')
+            touchp('dest/a/b/y')
+
+            self.link_tree.merge('dest')
+
+            self.check_file_link('dest/1')
+            self.check_file_link('dest/a/b/2')
+            self.check_file_link('dest/a/b/3')
+            self.check_file_link('dest/c/4')
+            self.check_file_link('dest/c/d/5')
+            self.check_file_link('dest/c/d/6')
+            self.check_file_link('dest/c/d/e/7')
+
+            self.assertTrue(os.path.isfile('dest/x'))
+            self.assertTrue(os.path.isfile('dest/a/b/y'))
+
+            self.link_tree.unmerge('dest')
+
+            self.assertTrue(os.path.isfile('dest/x'))
+            self.assertTrue(os.path.isfile('dest/a/b/y'))
+
+            self.assertFalse(os.path.isfile('dest/1'))
+            self.assertFalse(os.path.isfile('dest/a/b/2'))
+            self.assertFalse(os.path.isfile('dest/a/b/3'))
+            self.assertFalse(os.path.isfile('dest/c/4'))
+            self.assertFalse(os.path.isfile('dest/c/d/5'))
+            self.assertFalse(os.path.isfile('dest/c/d/6'))
+            self.assertFalse(os.path.isfile('dest/c/d/e/7'))
+
+
+    def test_merge_with_empty_directories(self):
+        with working_dir(self.stage.path):
+            mkdirp('dest/f/g')
+            mkdirp('dest/a/b/h')
+
+            self.link_tree.merge('dest')
+            self.link_tree.unmerge('dest')
+
+            self.assertFalse(os.path.exists('dest/1'))
+            self.assertFalse(os.path.exists('dest/a/b/2'))
+            self.assertFalse(os.path.exists('dest/a/b/3'))
+            self.assertFalse(os.path.exists('dest/c/4'))
+            self.assertFalse(os.path.exists('dest/c/d/5'))
+            self.assertFalse(os.path.exists('dest/c/d/6'))
+            self.assertFalse(os.path.exists('dest/c/d/e/7'))
+
+            self.assertTrue(os.path.isdir('dest/a/b/h'))
+            self.assertTrue(os.path.isdir('dest/f/g'))
+
+
+    def test_ignore(self):
+        with working_dir(self.stage.path):
+            touchp('source/.spec')
+            touchp('dest/.spec')
+
+            self.link_tree.merge('dest', ignore=lambda x: x == '.spec')
+            self.link_tree.unmerge('dest', ignore=lambda x: x == '.spec')
+
+            self.assertFalse(os.path.exists('dest/1'))
+            self.assertFalse(os.path.exists('dest/a'))
+            self.assertFalse(os.path.exists('dest/c'))
+
+            self.assertTrue(os.path.isfile('source/.spec'))
+            self.assertTrue(os.path.isfile('dest/.spec'))
diff --git a/var/spack/packages/R/package.py b/var/spack/packages/R/package.py
new file mode 100644
index 0000000000..2e6f65a742
--- /dev/null
+++ b/var/spack/packages/R/package.py
@@ -0,0 +1,33 @@
+from spack import *
+
+class R(Package):
+    """R is 'GNU S', a freely available language and environment for
+       statistical computing and graphics which provides a wide va
+       riety of statistical and graphical techniques: linear and
+       nonlinear modelling, statistical tests, time series analysis,
+       classification, clustering, etc. Please consult the R project
+       homepage for further information."""
+    homepage = "http://www.example.com"
+    url      = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz"
+
+    version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74')
+
+    depends_on("readline")
+    depends_on("ncurses")
+    depends_on("icu")
+    depends_on("glib")
+    depends_on("zlib")
+    depends_on("libtiff")
+    depends_on("jpeg")
+    depends_on("cairo")
+    depends_on("pango")
+    depends_on("freetype")
+    depends_on("tcl")
+    depends_on("tk")
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix,
+                  "--enable-R-shlib",
+                  "--enable-BLAS-shlib")
+        make()
+        make("install")
diff --git a/var/spack/packages/geos/package.py b/var/spack/packages/geos/package.py
new file mode 100644
index 0000000000..4a2657e32f
--- /dev/null
+++ b/var/spack/packages/geos/package.py
@@ -0,0 +1,31 @@
+from spack import *
+
+class Geos(Package):
+    """GEOS (Geometry Engine - Open Source) is a C++ port of the Java
+       Topology Suite (JTS). As such, it aims to contain the complete
+       functionality of JTS in C++. This includes all the OpenGIS
+       Simple Features for SQL spatial predicate functions and spatial
+       operators, as well as specific JTS enhanced topology functions."""
+
+    homepage = "http://trac.osgeo.org/geos/"
+    url      = "http://download.osgeo.org/geos/geos-3.4.2.tar.bz2"
+
+    version('3.4.2', 'fc5df2d926eb7e67f988a43a92683bae')
+    version('3.4.1', '4c930dec44c45c49cd71f3e0931ded7e')
+    version('3.4.0', 'e41318fc76b5dc764a69d43ac6b18488')
+    version('3.3.9', '4794c20f07721d5011c93efc6ccb8e4e')
+    version('3.3.8', '75be476d0831a2d14958fed76ca266de')
+    version('3.3.7', '95ab996d22672b067d92c7dee2170460')
+    version('3.3.6', '6fadfb941541875f4976f75fb0bbc800')
+    version('3.3.5', '2ba61afb7fe2c5ddf642d82d7b16e75b')
+    version('3.3.4', '1bb9f14d57ef06ffa41cb1d67acb55a1')
+    version('3.3.3', '8454e653d7ecca475153cc88fd1daa26')
+
+    extends('python')
+    depends_on('swig')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix,
+                  "--enable-python")
+        make()
+        make("install")
diff --git a/var/spack/packages/hdf5/package.py b/var/spack/packages/hdf5/package.py
index 615c2a7fe4..992dd8ec70 100644
--- a/var/spack/packages/hdf5/package.py
+++ b/var/spack/packages/hdf5/package.py
@@ -18,12 +18,14 @@ class Hdf5(Package):
 
     # TODO: currently hard-coded to use OpenMPI
     def install(self, spec, prefix):
+
         configure(
             "--prefix=%s" % prefix,
             "--with-zlib=%s" % spec['zlib'].prefix,
             "--enable-parallel",
-            "CC=%s" % spec['openmpi'].prefix.bin + "/mpicc",
-            "CXX=%s" % spec['openmpi'].prefix.bin + "/mpic++")
+            "--enable-shared",
+            "CC=%s" % spec['mpich'].prefix.bin + "/mpicc",
+            "CXX=%s" % spec['mpich'].prefix.bin + "/mpic++")
 
         make()
         make("install")
diff --git a/var/spack/packages/libgcrypt/package.py b/var/spack/packages/libgcrypt/package.py
new file mode 100644
index 0000000000..1d0a57f317
--- /dev/null
+++ b/var/spack/packages/libgcrypt/package.py
@@ -0,0 +1,19 @@
+from spack import *
+
+class Libgcrypt(Package):
+    """Libgcrypt is a general purpose cryptographic library based on
+       the code from GnuPG. It provides functions for all cryptographic
+       building blocks: symmetric ciphers, hash algorithms, MACs, public
+       key algorithms, large integer functions, random numbers and a lot
+       of supporting functions. """
+    homepage = "http://www.gnu.org/software/libgcrypt/"
+    url      = "ftp://ftp.gnupg.org/gcrypt/libgcrypt/libgcrypt-1.6.2.tar.bz2"
+
+    version('1.6.2', 'b54395a93cb1e57619943c082da09d5f')
+
+    depends_on("libgpg-error")
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+        make()
+        make("install")
diff --git a/var/spack/packages/libgpg-error/package.py b/var/spack/packages/libgpg-error/package.py
new file mode 100644
index 0000000000..6c1d1a10a7
--- /dev/null
+++ b/var/spack/packages/libgpg-error/package.py
@@ -0,0 +1,17 @@
+from spack import *
+
+class LibgpgError(Package):
+    """Libgpg-error is a small library that defines common error
+       values for all GnuPG components. Among these are GPG, GPGSM,
+       GPGME, GPG-Agent, libgcrypt, Libksba, DirMngr, Pinentry,
+       SmartCard Daemon and possibly more in the future. """
+
+    homepage = "https://www.gnupg.org/related_software/libgpg-error"
+    url      = "ftp://ftp.gnupg.org/gcrypt/libgpg-error/libgpg-error-1.18.tar.bz2"
+
+    version('1.18', '12312802d2065774b787cbfc22cc04e9')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+        make()
+        make("install")
diff --git a/var/spack/packages/libxml2/package.py b/var/spack/packages/libxml2/package.py
index 5eaed36d94..72199d8def 100644
--- a/var/spack/packages/libxml2/package.py
+++ b/var/spack/packages/libxml2/package.py
@@ -9,6 +9,9 @@ class Libxml2(Package):
 
     version('2.9.2', '9e6a9aca9d155737868b3dc5fd82f788')
 
+    depends_on('zlib')
+    depends_on('xz')
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix,
                   "--without-python")
diff --git a/var/spack/packages/libxslt/package.py b/var/spack/packages/libxslt/package.py
new file mode 100644
index 0000000000..f97332d020
--- /dev/null
+++ b/var/spack/packages/libxslt/package.py
@@ -0,0 +1,24 @@
+from spack import *
+
+class Libxslt(Package):
+    """Libxslt is the XSLT C library developed for the GNOME
+       project. XSLT itself is a an XML language to define
+       transformation for XML. Libxslt is based on libxml2 the XML C
+       library developed for the GNOME project. It also implements
+       most of the EXSLT set of processor-portable extensions
+       functions and some of Saxon's evaluate and expressions
+       extensions."""
+    homepage = "http://www.xmlsoft.org/XSLT/index.html"
+    url      = "http://xmlsoft.org/sources/libxslt-1.1.28.tar.gz"
+
+    version('1.1.28', '9667bf6f9310b957254fdcf6596600b7')
+
+    depends_on("libxml2")
+    depends_on("xz")
+    depends_on("zlib")
+    depends_on("libgcrypt")
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+        make()
+        make("install")
diff --git a/var/spack/packages/py-basemap/package.py b/var/spack/packages/py-basemap/package.py
new file mode 100644
index 0000000000..45f1085ba1
--- /dev/null
+++ b/var/spack/packages/py-basemap/package.py
@@ -0,0 +1,20 @@
+from spack import *
+import os
+
+class PyBasemap(Package):
+    """The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python."""
+    homepage = "http://matplotlib.org/basemap/"
+    url      = "https://downloads.sourceforge.net/project/matplotlib/matplotlib-toolkits/basemap-1.0.7/basemap-1.0.7.tar.gz"
+
+    version('1.0.7', '48c0557ced9e2c6e440b28b3caff2de8')
+
+    extends('python')
+    depends_on('py-setuptools')
+    depends_on('py-numpy')
+    depends_on('py-matplotlib')
+    depends_on('py-pil')
+    depends_on("geos")
+
+    def install(self, spec, prefix):
+        env['GEOS_DIR'] = spec['geos'].prefix
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-biopython/package.py b/var/spack/packages/py-biopython/package.py
new file mode 100644
index 0000000000..8ecaf48626
--- /dev/null
+++ b/var/spack/packages/py-biopython/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class PyBiopython(Package):
+    """It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics."""
+    homepage = "http://biopython.org/wiki/Main_Page"
+    url      = "http://biopython.org/DIST/biopython-1.65.tar.gz"
+
+    version('1.65', '143e7861ade85c0a8b5e2bbdd1da1f67')
+
+    extends('python')
+    depends_on('py-mx')
+    depends_on('py-numpy')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-cython/package.py b/var/spack/packages/py-cython/package.py
new file mode 100644
index 0000000000..af67a15526
--- /dev/null
+++ b/var/spack/packages/py-cython/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PyCython(Package):
+    """The Cython compiler for writing C extensions for the Python language."""
+    homepage = "https://pypi.python.org/pypi/cython"
+    url      = "https://pypi.python.org/packages/source/C/Cython/Cython-0.21.2.tar.gz"
+
+    version('0.21.2', 'd21adb870c75680dc857cd05d41046a4')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-dateutil/package.py b/var/spack/packages/py-dateutil/package.py
new file mode 100644
index 0000000000..11699e07ee
--- /dev/null
+++ b/var/spack/packages/py-dateutil/package.py
@@ -0,0 +1,14 @@
+from spack import *
+
+class PyDateutil(Package):
+    """Extensions to the standard Python datetime module."""
+    homepage = "https://pypi.python.org/pypi/dateutil"
+    url      = "https://pypi.python.org/packages/source/p/python-dateutil/python-dateutil-2.4.0.tar.gz"
+
+    version('2.4.0', '75714163bb96bedd07685cdb2071b8bc')
+
+    extends('python')
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-epydoc/package.py b/var/spack/packages/py-epydoc/package.py
new file mode 100644
index 0000000000..af05510504
--- /dev/null
+++ b/var/spack/packages/py-epydoc/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PyEpydoc(Package):
+    """Epydoc is a tool for generating API documentation documentation for Python modules, based on their docstrings."""
+    homepage = "https://pypi.python.org/pypi/epydoc"
+    url      = "https://pypi.python.org/packages/source/e/epydoc/epydoc-3.0.1.tar.gz"
+
+    version('3.0.1', '36407974bd5da2af00bf90ca27feeb44')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-gnuplot/package.py b/var/spack/packages/py-gnuplot/package.py
new file mode 100644
index 0000000000..ede4472c03
--- /dev/null
+++ b/var/spack/packages/py-gnuplot/package.py
@@ -0,0 +1,14 @@
+from spack import *
+
+class PyGnuplot(Package):
+    """Gnuplot.py is a Python package that allows you to create graphs from within Python using the gnuplot plotting program."""
+    homepage = "http://gnuplot-py.sourceforge.net/"
+    url      = "http://downloads.sourceforge.net/project/gnuplot-py/Gnuplot-py/1.8/gnuplot-py-1.8.tar.gz"
+
+    version('1.8', 'abd6f571e7aec68ae7db90a5217cd5b1')
+
+    extends('python')
+    depends_on('py-numpy')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-h5py/package.py b/var/spack/packages/py-h5py/package.py
new file mode 100644
index 0000000000..f72b3ac06e
--- /dev/null
+++ b/var/spack/packages/py-h5py/package.py
@@ -0,0 +1,18 @@
+from spack import *
+import re
+
+class PyH5py(Package):
+    """The h5py package provides both a high- and low-level interface to the HDF5 library from Python."""
+    homepage = "https://pypi.python.org/pypi/h5py"
+    url      = "https://pypi.python.org/packages/source/h/h5py/h5py-2.4.0.tar.gz"
+
+    version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758')
+
+    extends('python', ignore=lambda f: re.match(r'cy*', f))
+    depends_on('hdf5')
+    depends_on('py-numpy')
+    depends_on('py-cython')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'configure', '--hdf5=%s' % spec['hdf5'].prefix)
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-ipython/package.py b/var/spack/packages/py-ipython/package.py
new file mode 100644
index 0000000000..907ea9edcd
--- /dev/null
+++ b/var/spack/packages/py-ipython/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class PyIpython(Package):
+    """IPython provides a rich toolkit to help you make the most out of using Python interactively."""
+    homepage = "https://pypi.python.org/pypi/ipython"
+    url      = "https://pypi.python.org/packages/source/i/ipython/ipython-2.3.1.tar.gz"
+
+    version('2.3.1', '2b7085525dac11190bfb45bb8ec8dcbf')
+
+    extends('python')
+    depends_on('py-pygments')
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-libxml2/package.py b/var/spack/packages/py-libxml2/package.py
new file mode 100644
index 0000000000..59005428e4
--- /dev/null
+++ b/var/spack/packages/py-libxml2/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class PyLibxml2(Package):
+    """A Python wrapper around libxml2."""
+    homepage = "https://xmlsoft.org/python.html"
+    url      = "ftp://xmlsoft.org/libxml2/python/libxml2-python-2.6.21.tar.gz"
+
+    version('2.6.21', '229dd2b3d110a77defeeaa73af83f7f3')
+
+    extends('python')
+    depends_on('libxml2')
+    depends_on('libxslt')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-matplotlib/package.py b/var/spack/packages/py-matplotlib/package.py
new file mode 100644
index 0000000000..04037f004e
--- /dev/null
+++ b/var/spack/packages/py-matplotlib/package.py
@@ -0,0 +1,46 @@
+from spack import *
+import os
+
+class PyMatplotlib(Package):
+    """Python plotting package."""
+    homepage = "https://pypi.python.org/pypi/matplotlib"
+    url      = "https://pypi.python.org/packages/source/m/matplotlib/matplotlib-1.4.2.tar.gz"
+
+    version('1.4.2', '7d22efb6cce475025733c50487bd8898')
+
+    extends('python', ignore=r'bin/nosetests.*$')
+
+    depends_on('py-pyside')
+    depends_on('py-ipython')
+    depends_on('py-pyparsing')
+    depends_on('py-six')
+    depends_on('py-dateutil')
+    depends_on('py-pytz')
+    depends_on('py-nose')
+    depends_on('py-numpy')
+
+    depends_on('qt')
+    depends_on('bzip2')
+    depends_on('tcl')
+    depends_on('tk')
+    depends_on('qhull')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
+
+        if str(self.version) == '1.4.2':
+            # hack to fix configuration file
+            config_file = None
+            for p,d,f in os.walk(prefix.lib):
+                for file in f:
+                    if file.find('matplotlibrc') != -1:
+                        config_file = join_path(p, 'matplotlibrc')
+                        print config_file
+            if config_file == None:
+                raise InstallError('could not find config file')
+            filter_file(r'backend      : pyside',
+                        'backend      : Qt4Agg',
+                        config_file)
+            filter_file(r'#backend.qt4 : PyQt4',
+                        'backend.qt4 : PySide',
+                        config_file)
diff --git a/var/spack/packages/py-mpi4py/package.py b/var/spack/packages/py-mpi4py/package.py
new file mode 100644
index 0000000000..8001689a18
--- /dev/null
+++ b/var/spack/packages/py-mpi4py/package.py
@@ -0,0 +1,14 @@
+from spack import *
+
+class PyMpi4py(Package):
+    """This package provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI-1/MPI-2 specification and exposes an API which grounds on the standard MPI-2 C++ bindings."""
+    homepage = "https://pypi.python.org/pypi/mpi4py"
+    url      = "https://pypi.python.org/packages/source/m/mpi4py/mpi4py-1.3.1.tar.gz"
+
+    version('1.3.1', 'dbe9d22bdc8ed965c23a7ceb6f32fc3c')
+    extends('python')
+    depends_on('py-setuptools')
+    depends_on('mpi')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-mx/package.py b/var/spack/packages/py-mx/package.py
new file mode 100644
index 0000000000..717ee0562b
--- /dev/null
+++ b/var/spack/packages/py-mx/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PyMx(Package):
+    """The eGenix.com mx Base Distribution for Python is a collection of professional quality software tools which enhance Python's usability in many important areas such as fast text searching, date/time processing and high speed data types."""
+    homepage = "http://www.egenix.com/products/python/mxBase/"
+    url      = "https://downloads.egenix.com/python/egenix-mx-base-3.2.8.tar.gz"
+
+    version('3.2.8', '9d9d3a25f9dc051a15e97f452413423b')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-nose/package.py b/var/spack/packages/py-nose/package.py
new file mode 100644
index 0000000000..155019289d
--- /dev/null
+++ b/var/spack/packages/py-nose/package.py
@@ -0,0 +1,16 @@
+from spack import *
+
+class PyNose(Package):
+    """nose extends the test loading and running features of unittest,
+    making it easier to write, find and run tests."""
+
+    homepage = "https://pypi.python.org/pypi/nose"
+    url      = "https://pypi.python.org/packages/source/n/nose/nose-1.3.4.tar.gz"
+
+    version('1.3.4', '6ed7169887580ddc9a8e16048d38274d')
+
+    extends('python', ignore=r'bin/nosetests.*$')
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-numpy/package.py b/var/spack/packages/py-numpy/package.py
new file mode 100644
index 0000000000..e6cb6a464f
--- /dev/null
+++ b/var/spack/packages/py-numpy/package.py
@@ -0,0 +1,14 @@
+from spack import *
+
+class PyNumpy(Package):
+    """array processing for numbers, strings, records, and objects."""
+    homepage = "https://pypi.python.org/pypi/numpy"
+    url      = "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz"
+
+    version('1.9.1', '78842b73560ec378142665e712ae4ad9')
+
+    extends('python')
+    depends_on('py-nose')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-pexpect/package.py b/var/spack/packages/py-pexpect/package.py
new file mode 100644
index 0000000000..ff5fac84e0
--- /dev/null
+++ b/var/spack/packages/py-pexpect/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PyPexpect(Package):
+    """Pexpect allows easy control of interactive console applications."""
+    homepage = "https://pypi.python.org/pypi/pexpect"
+    url      = "https://pypi.python.org/packages/source/p/pexpect/pexpect-3.3.tar.gz"
+
+    version('3.3', '0de72541d3f1374b795472fed841dce8')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-pil/package.py b/var/spack/packages/py-pil/package.py
new file mode 100644
index 0000000000..743b761981
--- /dev/null
+++ b/var/spack/packages/py-pil/package.py
@@ -0,0 +1,14 @@
+from spack import *
+
+class PyPil(Package):
+    """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities."""
+
+    homepage = "http://www.pythonware.com/products/pil/"
+    url      = "http://effbot.org/media/downloads/Imaging-1.1.7.tar.gz"
+
+    version('1.1.7', 'fc14a54e1ce02a0225be8854bfba478e')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-pmw/package.py b/var/spack/packages/py-pmw/package.py
new file mode 100644
index 0000000000..56131811e9
--- /dev/null
+++ b/var/spack/packages/py-pmw/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PyPmw(Package):
+    """Pmw is a toolkit for building high-level compound widgets, or megawidgets, constructed using other widgets as component parts."""
+    homepage = "https://pypi.python.org/pypi/Pmw"
+    url      = "https://pypi.python.org/packages/source/P/Pmw/Pmw-2.0.0.tar.gz"
+
+    version('2.0.0', 'c7c3f26c4f5abaa99807edefee578fc0')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-pychecker/package.py b/var/spack/packages/py-pychecker/package.py
new file mode 100644
index 0000000000..bda5a746aa
--- /dev/null
+++ b/var/spack/packages/py-pychecker/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PyPychecker(Package):
+    """"""
+    homepage = "http://pychecker.sourceforge.net/"
+    url      = "http://sourceforge.net/projects/pychecker/files/pychecker/0.8.19/pychecker-0.8.19.tar.gz"
+
+    version('0.8.19', 'c37182863dfb09209d6ba4f38fce9d2b')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-pygments/package.py b/var/spack/packages/py-pygments/package.py
new file mode 100644
index 0000000000..990eebde65
--- /dev/null
+++ b/var/spack/packages/py-pygments/package.py
@@ -0,0 +1,14 @@
+from spack import *
+
+class PyPygments(Package):
+    """Pygments is a syntax highlighting package written in Python."""
+    homepage = "https://pypi.python.org/pypi/pygments"
+    url      = "https://pypi.python.org/packages/source/P/Pygments/Pygments-2.0.1.tar.gz"
+
+    version('2.0.1', 'e0daf4c14a4fe5b630da765904de4d6c')
+
+    extends('python')
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-pylint/package.py b/var/spack/packages/py-pylint/package.py
new file mode 100644
index 0000000000..7a6ee7dbbc
--- /dev/null
+++ b/var/spack/packages/py-pylint/package.py
@@ -0,0 +1,16 @@
+from spack import *
+import re
+
+class PyPylint(Package):
+    """array processing for numbers, strings, records, and objects."""
+    homepage = "https://pypi.python.org/pypi/pylint"
+    url      = "https://pypi.python.org/packages/source/p/pylint/pylint-1.4.1.tar.gz"
+
+    version('1.4.1', 'df7c679bdcce5019389038847e4de622')
+
+    extends('python')
+    depends_on('py-nose')
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-pyparsing/package.py b/var/spack/packages/py-pyparsing/package.py
new file mode 100644
index 0000000000..a6e50ad139
--- /dev/null
+++ b/var/spack/packages/py-pyparsing/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PyPyparsing(Package):
+    """A Python Parsing Module."""
+    homepage = "https://pypi.python.org/pypi/pyparsing"
+    url      = "https://pypi.python.org/packages/source/p/pyparsing/pyparsing-2.0.3.tar.gz"
+
+    version('2.0.3', '0fe479be09fc2cf005f753d3acc35939')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-pyqt/package.py b/var/spack/packages/py-pyqt/package.py
new file mode 100644
index 0000000000..8edca105bb
--- /dev/null
+++ b/var/spack/packages/py-pyqt/package.py
@@ -0,0 +1,24 @@
+from spack import *
+
+class PyPyqt(Package):
+    """PyQt is a set of Python v2 and v3 bindings for Digia's Qt
+       application framework and runs on all platforms supported by Qt
+       including Windows, MacOS/X and Linux."""
+    homepage = "http://www.riverbankcomputing.com/software/pyqt/intro"
+    url      = "http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-4.11.3/PyQt-x11-gpl-4.11.3.tar.gz"
+
+    version('4.11.3', '997c3e443165a89a559e0d96b061bf70')
+
+    extends('python')
+    depends_on('py-sip')
+
+    # TODO: allow qt5 when conditional deps are supported.
+    # TODO: Fix version matching so that @4 works like @:4
+    depends_on('qt@:4')
+
+    def install(self, spec, prefix):
+        python('configure.py',
+               '--confirm-license',
+               '--destdir=%s' % site_packages_dir)
+        make()
+        make('install')
diff --git a/var/spack/packages/py-pyside/package.py b/var/spack/packages/py-pyside/package.py
new file mode 100644
index 0000000000..6583431124
--- /dev/null
+++ b/var/spack/packages/py-pyside/package.py
@@ -0,0 +1,47 @@
+from spack import *
+import os
+
+class PyPyside(Package):
+    """array processing for numbers, strings, records, and objects."""
+    homepage = "https://pypi.python.org/pypi/pyside"
+    url      = "https://pypi.python.org/packages/source/P/PySide/PySide-1.2.2.tar.gz"
+
+    version('1.2.2', 'c45bc400c8a86d6b35f34c29e379e44d')
+
+    # TODO: make build dependency
+    # depends_on("cmake")
+
+    extends('python')
+    depends_on('py-setuptools')
+    depends_on('qt@:4')
+
+    def patch(self):
+        """Undo PySide RPATH handling and add Spack RPATH."""
+        # Figure out the special RPATH
+        pypkg = self.spec['python'].package
+        rpath = self.rpath
+        rpath.append(os.path.join(self.prefix, pypkg.site_packages_dir, 'PySide'))
+
+        # Add Spack's standard CMake args to the sub-builds.
+        # They're called BY setup.py so we have to patch it.
+        filter_file(
+            r'OPTION_CMAKE,',
+            r'OPTION_CMAKE, ' + (
+                '"-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE", '
+                '"-DCMAKE_INSTALL_RPATH=%s",' % ':'.join(rpath)),
+            'setup.py')
+
+        # PySide tries to patch ELF files to remove RPATHs
+        # Disable this and go with the one we set.
+        filter_file(
+            r'^\s*rpath_cmd\(pyside_path, srcpath\)',
+            r'#rpath_cmd(pyside_path, srcpath)',
+            'pyside_postinstall.py')
+
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install',
+               '--prefix=%s' % prefix,
+               '--jobs=%s' % make_jobs)
+
+
diff --git a/var/spack/packages/py-pytz/package.py b/var/spack/packages/py-pytz/package.py
new file mode 100644
index 0000000000..80bcfe82ca
--- /dev/null
+++ b/var/spack/packages/py-pytz/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PyPytz(Package):
+    """World timezone definitions, modern and historical."""
+    homepage = "https://pypi.python.org/pypi/pytz"
+    url      = "https://pypi.python.org/packages/source/p/pytz/pytz-2014.10.tar.gz"
+
+    version('2014.10', 'eb1cb941a20c5b751352c52486aa1dd7')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-rpy2/package.py b/var/spack/packages/py-rpy2/package.py
new file mode 100644
index 0000000000..dd0c0672af
--- /dev/null
+++ b/var/spack/packages/py-rpy2/package.py
@@ -0,0 +1,16 @@
+from spack import *
+
+class PyRpy2(Package):
+    """rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions."""
+    homepage = "https://pypi.python.org/pypi/rpy2"
+    url      = "https://pypi.python.org/packages/source/r/rpy2/rpy2-2.5.4.tar.gz"
+
+    version('2.5.4', '115a20ac30883f096da2bdfcab55196d')
+
+    extends('python')
+    depends_on('py-setuptools')
+
+    depends_on('R')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-scientificpython/package.py b/var/spack/packages/py-scientificpython/package.py
new file mode 100644
index 0000000000..020d830703
--- /dev/null
+++ b/var/spack/packages/py-scientificpython/package.py
@@ -0,0 +1,17 @@
+from spack import *
+
+class PyScientificpython(Package):
+    """ScientificPython is a collection of Python modules for
+       scientific computing. It contains support for geometry,
+       mathematical functions, statistics, physical units, IO,
+       visualization, and parallelization."""
+
+    homepage = "https://sourcesup.renater.fr/projects/scientific-py/"
+    url      = "https://sourcesup.renater.fr/frs/download.php/4411/ScientificPython-2.8.1.tar.gz"
+
+    version('2.8.1', '73ee0df19c7b58cdf2954261f0763c77')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-scikit-learn/package.py b/var/spack/packages/py-scikit-learn/package.py
new file mode 100644
index 0000000000..c59c05a619
--- /dev/null
+++ b/var/spack/packages/py-scikit-learn/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PyScikitLearn(Package):
+    """"""
+    homepage = "https://pypi.python.org/pypi/scikit-learn"
+    url      = "https://pypi.python.org/packages/source/s/scikit-learn/scikit-learn-0.15.2.tar.gz"
+
+    version('0.15.2', 'd9822ad0238e17b382a3c756ea94fe0d')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-scipy/package.py b/var/spack/packages/py-scipy/package.py
new file mode 100644
index 0000000000..b5325b919f
--- /dev/null
+++ b/var/spack/packages/py-scipy/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class PyScipy(Package):
+    """Scientific Library for Python."""
+    homepage = "https://pypi.python.org/pypi/scipy"
+    url      = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz"
+
+    version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a')
+
+    extends('python')
+    depends_on('py-nose')
+    depends_on('py-numpy')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-setuptools/package.py b/var/spack/packages/py-setuptools/package.py
new file mode 100644
index 0000000000..755288d55c
--- /dev/null
+++ b/var/spack/packages/py-setuptools/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PySetuptools(Package):
+    """Easily download, build, install, upgrade, and uninstall Python packages."""
+    homepage = "https://pypi.python.org/pypi/setuptools"
+    url      = "https://pypi.python.org/packages/source/s/setuptools/setuptools-11.3.tar.gz"
+
+    version('11.3.1', '01f69212e019a2420c1693fb43593930')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-shiboken/package.py b/var/spack/packages/py-shiboken/package.py
new file mode 100644
index 0000000000..e4bf4ce07e
--- /dev/null
+++ b/var/spack/packages/py-shiboken/package.py
@@ -0,0 +1,45 @@
+from spack import *
+import os
+
+class PyShiboken(Package):
+    """Shiboken generates bindings for C++ libraries using CPython source code."""
+    homepage = "https://shiboken.readthedocs.org/"
+    url      = "https://pypi.python.org/packages/source/S/Shiboken/Shiboken-1.2.2.tar.gz"
+
+    version('1.2.2', '345cfebda221f525842e079a6141e555')
+
+    # TODO: make build dependency
+    # depends_on("cmake")
+
+    extends('python')
+    depends_on("py-setuptools")
+    depends_on("libxml2")
+    depends_on("qt@:4.8")
+
+    def patch(self):
+        """Undo Shiboken RPATH handling and add Spack RPATH."""
+        # Add Spack's standard CMake args to the sub-builds.
+        # They're called BY setup.py so we have to patch it.
+        pypkg = self.spec['python'].package
+        rpath = self.rpath
+        rpath.append(os.path.join(self.prefix, pypkg.site_packages_dir, 'Shiboken'))
+
+        filter_file(
+            r'OPTION_CMAKE,',
+            r'OPTION_CMAKE, ' + (
+                '"-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE", '
+                '"-DCMAKE_INSTALL_RPATH=%s",' % ':'.join(rpath)),
+            'setup.py')
+
+        # Shiboken tries to patch ELF files to remove RPATHs
+        # Disable this and go with the one we set.
+        filter_file(
+            r'^\s*rpath_cmd\(shiboken_path, srcpath\)',
+            r'#rpath_cmd(shiboken_path, srcpath)',
+            'shiboken_postinstall.py')
+
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install',
+               '--prefix=%s' % prefix,
+               '--jobs=%s' % make_jobs)
diff --git a/var/spack/packages/py-sip/package.py b/var/spack/packages/py-sip/package.py
new file mode 100644
index 0000000000..6753bdd2a5
--- /dev/null
+++ b/var/spack/packages/py-sip/package.py
@@ -0,0 +1,20 @@
+from spack import *
+import os
+
+class PySip(Package):
+    """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries."""
+    homepage = "http://www.riverbankcomputing.com/software/sip/intro"
+    url      = "http://sourceforge.net/projects/pyqt/files/sip/sip-4.16.5/sip-4.16.5.tar.gz"
+
+    version('4.16.5', '6d01ea966a53e4c7ae5c5e48c40e49e5')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('configure.py',
+               '--destdir=%s' % site_packages_dir,
+               '--bindir=%s' % spec.prefix.bin,
+               '--incdir=%s' % python_include_dir,
+               '--sipdir=%s' % os.path.join(spec.prefix.share, 'sip'))
+        make()
+        make('install')
diff --git a/var/spack/packages/py-six/package.py b/var/spack/packages/py-six/package.py
new file mode 100644
index 0000000000..04d29adced
--- /dev/null
+++ b/var/spack/packages/py-six/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PySix(Package):
+    """Python 2 and 3 compatibility utilities."""
+    homepage = "https://pypi.python.org/pypi/six"
+    url      = "https://pypi.python.org/packages/source/s/six/six-1.9.0.tar.gz"
+
+    version('1.9.0', '476881ef4012262dfc8adc645ee786c4')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-sympy/package.py b/var/spack/packages/py-sympy/package.py
new file mode 100644
index 0000000000..c17e35b95f
--- /dev/null
+++ b/var/spack/packages/py-sympy/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PySympy(Package):
+    """SymPy is a Python library for symbolic mathematics."""
+    homepage = "https://pypi.python.org/pypi/sympy"
+    url      = "https://pypi.python.org/packages/source/s/sympy/sympy-0.7.6.tar.gz"
+
+    version('0.7.6', '3d04753974306d8a13830008e17babca')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-virtualenv/package.py b/var/spack/packages/py-virtualenv/package.py
new file mode 100644
index 0000000000..9d94c2dcda
--- /dev/null
+++ b/var/spack/packages/py-virtualenv/package.py
@@ -0,0 +1,19 @@
+from spack import *
+import shutil
+
+class PyVirtualenv(Package):
+    """virtualenv is a tool to create isolated Python environments."""
+    homepage = "http://virtualenv.readthedocs.org/projects/virtualenv/"
+    url      = "https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.11.6.tar.gz"
+
+    version('1.11.6', 'f61cdd983d2c4e6aeabb70b1060d6f49')
+
+    extends('python')
+    depends_on('py-setuptools')
+
+    def clean(self):
+        if os.path.exists('build'):
+            shutil.rmtree('build')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/python/package.py b/var/spack/packages/python/package.py
index e6c3e28820..31a12ea653 100644
--- a/var/spack/packages/python/package.py
+++ b/var/spack/packages/python/package.py
@@ -1,10 +1,19 @@
+import os
+import re
+from contextlib import closing
+from llnl.util.lang import match_predicate
+
 from spack import *
+import spack
+
 
 class Python(Package):
     """The Python programming language."""
     homepage = "http://www.python.org"
     url      = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tar.xz"
 
+    extendable = True
+
     version('2.7.8', 'd235bdfa75b8396942e360a70487ee00')
 
     depends_on("openssl")
@@ -23,3 +32,126 @@ class Python(Package):
                   "--enable-shared")
         make()
         make("install")
+
+
+    # ========================================================================
+    # Set up environment to make install easy for python extensions.
+    # ========================================================================
+
+    @property
+    def python_lib_dir(self):
+        return os.path.join('lib', 'python%d.%d' % self.version[:2])
+
+
+    @property
+    def python_include_dir(self):
+        return os.path.join('include', 'python%d.%d' % self.version[:2])
+
+
+    @property
+    def site_packages_dir(self):
+        return os.path.join(self.python_lib_dir, 'site-packages')
+
+
+    def setup_dependent_environment(self, module, spec, ext_spec):
+        """Called before python modules' install() methods.
+
+        In most cases, extensions will only need to have one line::
+
+            python('setup.py', 'install', '--prefix=%s' % prefix)
+        """
+        # Python extension builds can have a global python executable function
+        module.python = Executable(join_path(spec.prefix.bin, 'python'))
+
+        # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs.
+        module.python_lib_dir     = os.path.join(ext_spec.prefix, self.python_lib_dir)
+        module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir)
+        module.site_packages_dir  = os.path.join(ext_spec.prefix, self.site_packages_dir)
+
+        # Make the site packages directory if it does not exist already.
+        mkdirp(module.site_packages_dir)
+
+        # Set PYTHONPATH to include site-packages dir for the
+        # extension and any other python extensions it depends on.
+        python_paths = []
+        for d in ext_spec.traverse():
+            if d.package.extends(self.spec):
+                python_paths.append(os.path.join(d.prefix, self.site_packages_dir))
+        os.environ['PYTHONPATH'] = ':'.join(python_paths)
+
+
+    # ========================================================================
+    # Handle specifics of activating and deactivating python modules.
+    # ========================================================================
+
+    def python_ignore(self, ext_pkg, args):
+        """Add some ignore files to activate/deactivate args."""
+        ignore_arg = args.get('ignore', lambda f: False)
+
+        # Always ignore easy-install.pth, as it needs to be merged.
+        patterns = [r'easy-install\.pth$']
+
+        # Ignore pieces of setuptools installed by other packages.
+        if ext_pkg.name != 'py-setuptools':
+            patterns.append(r'/site\.pyc?$')
+            patterns.append(r'setuptools\.pth')
+            patterns.append(r'bin/easy_install[^/]*$')
+            patterns.append(r'setuptools.*egg$')
+
+        return match_predicate(ignore_arg, patterns)
+
+
+    def write_easy_install_pth(self, exts):
+        paths = []
+        for ext in sorted(exts.values()):
+            ext_site_packages = os.path.join(ext.prefix, self.site_packages_dir)
+            easy_pth = "%s/easy-install.pth" % ext_site_packages
+
+            if not os.path.isfile(easy_pth):
+                continue
+
+            with closing(open(easy_pth)) as f:
+                for line in f:
+                    line = line.rstrip()
+
+                    # Skip lines matching these criteria
+                    if not line: continue
+                    if re.search(r'^(import|#)', line): continue
+                    if (ext.name != 'py-setuptools' and
+                        re.search(r'setuptools.*egg$', line)): continue
+
+                    paths.append(line)
+
+        site_packages = os.path.join(self.prefix, self.site_packages_dir)
+        main_pth = "%s/easy-install.pth" % site_packages
+
+        if not paths:
+            if os.path.isfile(main_pth):
+                os.remove(main_pth)
+
+        else:
+            with closing(open(main_pth, 'w')) as f:
+                f.write("import sys; sys.__plen = len(sys.path)\n")
+                for path in paths:
+                    f.write("%s\n" % path)
+                f.write("import sys; new=sys.path[sys.__plen:]; del sys.path[sys.__plen:]; "
+                        "p=getattr(sys,'__egginsert',0); sys.path[p:p]=new; sys.__egginsert = p+len(new)\n")
+
+
+    def activate(self, ext_pkg, **args):
+        args.update(ignore=self.python_ignore(ext_pkg, args))
+        super(Python, self).activate(ext_pkg, **args)
+
+        exts = spack.install_layout.extension_map(self.spec)
+        exts[ext_pkg.name] = ext_pkg.spec
+        self.write_easy_install_pth(exts)
+
+
+    def deactivate(self, ext_pkg, **args):
+        args.update(ignore=self.python_ignore(ext_pkg, args))
+        super(Python, self).deactivate(ext_pkg, **args)
+
+        exts = spack.install_layout.extension_map(self.spec)
+        if ext_pkg.name in exts:        # Make deactivate idempotent.
+            del exts[ext_pkg.name]
+            self.write_easy_install_pth(exts)
diff --git a/var/spack/packages/qhull/package.py b/var/spack/packages/qhull/package.py
new file mode 100644
index 0000000000..9da4078a70
--- /dev/null
+++ b/var/spack/packages/qhull/package.py
@@ -0,0 +1,27 @@
+from spack import *
+
+class Qhull(Package):
+    """Qhull computes the convex hull, Delaunay triangulation, Voronoi
+       diagram, halfspace intersection about a point, furt hest-site
+       Delaunay triangulation, and furthest-site Voronoi diagram. The
+       source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull
+       implements the Quickhull algorithm for computing the convex
+       hull. It handles roundoff errors from floating point
+       arithmetic. It computes volumes, surface areas, and
+       approximations to the convex hull.
+
+       Qhull does not support triangulation of non-convex surfaces,
+       mesh generation of non-convex objects, medium-sized inputs in
+       9-D and higher, alpha shapes, weighted Voronoi diagrams,
+       Voronoi volumes, or constrained Delaunay triangulations."""
+
+    homepage = "http://www.qhull.org"
+
+    version('1.0', 'd0f978c0d8dfb2e919caefa56ea2953c',
+            url="http://www.qhull.org/download/qhull-2012.1-src.tgz")
+
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+            cmake('..', *std_cmake_args)
+            make()
+            make("install")
diff --git a/var/spack/packages/qt/package.py b/var/spack/packages/qt/package.py
index 01f9de7f3c..3b5096c4f0 100644
--- a/var/spack/packages/qt/package.py
+++ b/var/spack/packages/qt/package.py
@@ -1,3 +1,4 @@
+import os
 from spack import *
 
 class Qt(Package):
@@ -20,6 +21,11 @@ class Qt(Package):
     depends_on("libmng")
     depends_on("jpeg")
 
+    def setup_dependent_environment(self, module, spec, dep_spec):
+        """Dependencies of Qt find it using the QTDIR environment variable."""
+        os.environ['QTDIR'] = self.prefix
+
+
     def patch(self):
         # Fix qmake compilers in the default mkspec
         qmake_conf = 'mkspecs/common/g++-base.conf'
@@ -37,8 +43,9 @@ class Qt(Package):
                   '-fast',
                   '-optimized-qmake',
                   '-no-pch',
-                  '-no-phonon',
-                  '-no-phonon-backend',
+                  # phonon required for py-pyqt
+                  # '-no-phonon',
+                  # '-no-phonon-backend',
                   '-no-openvg')
         make()
         make("install")
diff --git a/var/spack/packages/tcl/package.py b/var/spack/packages/tcl/package.py
new file mode 100644
index 0000000000..529adf7788
--- /dev/null
+++ b/var/spack/packages/tcl/package.py
@@ -0,0 +1,22 @@
+from spack import *
+
+class Tcl(Package):
+    """Tcl (Tool Command Language) is a very powerful but easy to
+       learn dynamic programming language, suitable for a very wide
+       range of uses, including web and desktop applications,
+       networking, administration, testing and many more. Open source
+       and business-friendly, Tcl is a mature yet evolving language
+       that is truly cross platform, easily deployed and highly
+       extensible."""
+    homepage = "http://www.tcl.tk"
+
+    version('8.6.3', 'db382feca91754b7f93da16dc4cdad1f',
+            url="http://prdownloads.sourceforge.net/tcl/tcl8.6.3-src.tar.gz")
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        with working_dir('unix'):
+            configure("--prefix=%s" % prefix)
+            make()
+            make("install")
diff --git a/var/spack/packages/tk/package.py b/var/spack/packages/tk/package.py
new file mode 100644
index 0000000000..96736f6f95
--- /dev/null
+++ b/var/spack/packages/tk/package.py
@@ -0,0 +1,22 @@
+from spack import *
+
+class Tk(Package):
+    """Tk is a graphical user interface toolkit that takes developing
+       desktop applications to a higher level than conventional
+       approaches. Tk is the standard GUI not only for Tcl, but for
+       many other dynamic languages, and can produce rich, native
+       applications that run unchanged across Windows, Mac OS X, Linux
+       and more."""
+    homepage = "http://www.tcl.tk"
+    url      = "http://prdownloads.sourceforge.net/tcl/tk8.6.3-src.tar.gz"
+
+    version('src', '85ca4dbf4dcc19777fd456f6ee5d0221')
+
+    depends_on("tcl")
+
+    def install(self, spec, prefix):
+        with working_dir('unix'):
+            configure("--prefix=%s" % prefix,
+                      "--with-tcl=%s" % spec['tcl'].prefix.lib)
+            make()
+            make("install")