From 88afad3e46326c56aaeaed6adc2058033ad7ad33 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 6 Jan 2015 14:47:51 -0500
Subject: Directory layout can now track installed extensions per package.

---
 lib/spack/spack/directory_layout.py | 97 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 96 insertions(+), 1 deletion(-)

diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index 42cac0c9d2..4ab9a515cf 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -71,6 +71,21 @@ class DirectoryLayout(object):
         raise NotImplementedError()
 
 
+    def get_extensions(self, spec):
+        """Get a set of currently installed extension packages for a spec."""
+        raise NotImplementedError()
+
+
+    def add_extension(self, spec, extension_spec):
+        """Add to the list of currently installed extensions."""
+        raise NotImplementedError()
+
+
+    def remove_extension(self, spec, extension_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)
@@ -134,9 +149,11 @@ 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
 
 
     def relative_path_for_spec(self, spec):
@@ -225,6 +242,55 @@ class SpecHashDirectoryLayout(DirectoryLayout):
                 yield spec
 
 
+    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 get_extensions(self, spec):
+        path = self.extension_file_path(spec)
+
+        extensions = set()
+        if os.path.exists(path):
+            with closing(open(path)) as spec_file:
+                for line in spec_file:
+                    try:
+                        extensions.add(Spec(line))
+                    except SpecError, e:
+                        raise InvalidExtensionSpecError(str(e))
+        return extensions
+
+
+    def write_extensions(self, extensions):
+        path = self.extension_file_path(spec)
+        with closing(open(path, 'w')) as spec_file:
+            for extension in sorted(extensions):
+                spec_file.write("%s\n" % extensions)
+
+
+    def add_extension(self, spec, extension_spec):
+        exts = get_extensions(spec)
+        if extension_spec in exts:
+            raise ExtensionAlreadyInstalledError(spec, extension_spec)
+        else:
+            for already_installed in exts:
+                if spec.name == extension_spec.name:
+                    raise ExtensionConflictError(spec, extension_spec, already_installed)
+
+        exts.add(extension_spec)
+        self.write_extensions(exts)
+
+
+    def remove_extension(self, spec, extension_spec):
+        exts = get_extensions(spec)
+        if not extension_spec in exts:
+            raise NoSuchExtensionError(spec, extension_spec)
+
+        exts.remove(extension_spec)
+        self.write_extensions(exts)
+
+
 class DirectoryLayoutError(SpackError):
     """Superclass for directory layout errors."""
     def __init__(self, message):
@@ -250,3 +316,32 @@ 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, extension_spec):
+        super(ExtensionAlreadyInstalledError, self).__init__(
+            "%s is already installed in %s" % (extension_spec, spec))
+
+
+class ExtensionConflictError(DirectoryLayoutError):
+    """Raised when an extension is added to a package that already has it."""
+    def __init__(self, spec, extension_spec, conflict):
+        super(ExtensionConflictError, self).__init__(
+            "%s cannot be installed in %s because it conflicts with %s."% (
+                extension_spec, spec, conflict))
+
+
+class NoSuchExtensionError(DirectoryLayoutError):
+    """Raised when an extension isn't there on remove."""
+    def __init__(self, spec, extension_spec):
+        super(NoSuchExtensionError, self).__init__(
+            "%s cannot be removed from %s beacuse it's not installed."% (
+                extension_spec, spec, conflict))
-- 
cgit v1.2.3-70-g09d2


From ebe0c1d83ac1380a6320a8dadcfa2ad4fc07c279 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 6 Jan 2015 14:49:13 -0500
Subject: New "extends" relation adds another special list to the package
 class.

---
 lib/spack/spack/package.py   |  3 +++
 lib/spack/spack/relations.py | 26 +++++++++++++++++++++++++-
 2 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 1dfd3d1c83..c256ea479f 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -314,6 +314,9 @@ class Package(object):
     """Specs of virtual packages provided by this package, keyed by name."""
     provided = {}
 
+    """Specs of packages this one extends, keyed by name."""
+    extendees = {}
+
     """Specs of conflicting packages, keyed by name. """
     conflicted = {}
 
diff --git a/lib/spack/spack/relations.py b/lib/spack/spack/relations.py
index b1f4348945..aaca9c199e 100644
--- a/lib/spack/spack/relations.py
+++ b/lib/spack/spack/relations.py
@@ -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 +117,29 @@ def depends_on(*specs):
             dependencies[spec.name] = spec
 
 
+def extends(*specs):
+    """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.
+
+    """
+    pkg = get_calling_package_name()
+    clocals = caller_locals()
+    dependencies = clocals.setdefault('dependencies', {})
+    extendees = clocals.setdefault('extendees', {})
+
+    for string in specs:
+        for spec in spack.spec.parse(string):
+            if pkg == spec.name:
+                raise CircularReferenceError('depends_on', pkg)
+            dependencies[spec.name] = spec
+            extendees[spec.name] = spec
+
+
 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
-- 
cgit v1.2.3-70-g09d2


From adb7d614e69a0c176c86b3b4aaa1e81d403d0a71 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 6 Jan 2015 14:50:14 -0500
Subject: Add pre-install and pre-uninstall hooks.

---
 lib/spack/spack/hooks/__init__.py | 7 ++++++-
 lib/spack/spack/package.py        | 8 ++++++++
 2 files changed, 14 insertions(+), 1 deletion(-)

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/package.py b/lib/spack/spack/package.py
index c256ea479f..aa79721266 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -768,6 +768,10 @@ class Package(object):
                 # 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)
@@ -862,6 +866,10 @@ 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)
 
-- 
cgit v1.2.3-70-g09d2


From 2c1eda66c4d7a0df8f0a05ad16be38942f54dcee Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 6 Jan 2015 14:50:40 -0500
Subject: First python extension package: setuptools

---
 var/spack/packages/py-setuptools/package.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 var/spack/packages/py-setuptools/package.py

diff --git a/var/spack/packages/py-setuptools/package.py b/var/spack/packages/py-setuptools/package.py
new file mode 100644
index 0000000000..e2c4e1a0be
--- /dev/null
+++ b/var/spack/packages/py-setuptools/package.py
@@ -0,0 +1,19 @@
+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):
+        site_packages_dir = "%s/lib/python2.7/site-packages" % prefix
+        mkdirp(site_packages_dir)
+
+        env['PYTHONPATH'] = site_packages_dir
+
+        python = which('python')
+        python('setup.py', 'install', '--prefix=%s' % prefix)
-- 
cgit v1.2.3-70-g09d2


From 7215aee224150d954e8a5bd6b632b6d8f66948d2 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 7 Jan 2015 17:45:14 -0500
Subject: do_install() passes kwargs to dependencies.

---
 lib/spack/spack/package.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index aa79721266..04f0d842da 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -744,7 +744,7 @@ 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:
@@ -832,10 +832,10 @@ class Package(object):
         spack.hooks.post_install(self)
 
 
-    def do_install_dependencies(self):
+    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
-- 
cgit v1.2.3-70-g09d2


From 99775434785779d223997a9e41972da470214e5d Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 7 Jan 2015 11:48:21 -0800
Subject: Added feature: package extensions

- packages can be "extended" by others
- allows extension to be symlinked into extendee's prefix.
- used for python modules.
  - first module: py-setuptools
---
 lib/spack/llnl/util/filesystem.py    | 82 +++++++++++++++++++++++++++++++++-
 lib/spack/spack/__init__.py          |  2 +-
 lib/spack/spack/directory_layout.py  | 55 ++++++++++++++++-------
 lib/spack/spack/hooks/extensions.py  | 49 +++++++++++++++++++++
 lib/spack/spack/package.py           | 85 ++++++++++++++++++++++++++++++++++++
 lib/spack/spack/relations.py         |  4 +-
 var/spack/packages/python/package.py |  3 ++
 7 files changed, 261 insertions(+), 19 deletions(-)
 create mode 100644 lib/spack/spack/hooks/extensions.py

diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index 0578415653..9fb76d3a35 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -24,7 +24,8 @@
 ##############################################################################
 __all__ = ['set_install_permissions', 'install', 'expand_user', 'working_dir',
            'touch', 'mkdirp', 'force_remove', 'join_path', 'ancestor',
-           'can_access', 'filter_file', 'change_sed_delimiter', 'is_exe']
+           'can_access', 'filter_file', 'change_sed_delimiter', 'is_exe',
+           'check_link_tree', 'merge_link_tree', 'unmerge_link_tree']
 
 import os
 import sys
@@ -222,3 +223,82 @@ def ancestor(dir, n=1):
 def can_access(file_name):
     """True if we have read/write access to the file."""
     return os.access(file_name, os.R_OK|os.W_OK)
+
+
+def traverse_link_tree(src_root, dest_root, follow_nonexisting=True, **kwargs):
+    # Yield directories before or after their contents.
+    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', None)
+    if isinstance(ignore, basestring):
+        ignore = (ignore,)
+
+    for dirpath, dirnames, filenames in os.walk(src_root):
+        rel_path  = dirpath[len(src_root):]
+        rel_path = rel_path.lstrip(os.path.sep)
+        dest_dirpath = os.path.join(dest_root, rel_path)
+
+        # Don't descend into ignored directories
+        if ignore and dest_dirpath in ignore:
+            return
+
+        # Don't descend into dirs in dest that do not exist in src.
+        if not follow_nonexisting:
+            dirnames[:] = [
+                d for d in dirnames
+                if os.path.exists(os.path.join(dest_dirpath, d))]
+
+        # preorder yields directories before children
+        if order == 'pre':
+            yield (dirpath, dest_dirpath)
+
+        for name in filenames:
+            src_file  = os.path.join(dirpath, name)
+            dest_file = os.path.join(dest_dirpath, name)
+
+            # Ignore particular paths inside the install root.
+            src_relpath = src_file[len(src_root):]
+            src_relpath = src_relpath.lstrip(os.path.sep)
+            if ignore and src_relpath in ignore:
+                continue
+
+            yield (src_file, dest_file)
+
+        # postorder yields directories after children
+        if order == 'post':
+            yield (dirpath, dest_dirpath)
+
+
+
+def check_link_tree(src_root, dest_root, **kwargs):
+    for src, dest in traverse_link_tree(src_root, dest_root, False, **kwargs):
+        if os.path.exists(dest) and not os.path.isdir(dest):
+            return dest
+    return None
+
+
+def merge_link_tree(src_root, dest_root, **kwargs):
+    kwargs['order'] = 'pre'
+    for src, dest in traverse_link_tree(src_root, dest_root, **kwargs):
+        if os.path.isdir(src):
+            mkdirp(dest)
+        else:
+            assert(not os.path.exists(dest))
+            os.symlink(src, dest)
+
+
+def unmerge_link_tree(src_root, dest_root, **kwargs):
+    kwargs['order'] = 'post'
+    for src, dest in traverse_link_tree(src_root, dest_root, **kwargs):
+        if os.path.isdir(dest):
+            if not os.listdir(dest):
+                # TODO: what if empty directories were present pre-merge?
+                shutil.rmtree(dest, ignore_errors=True)
+
+        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/directory_layout.py b/lib/spack/spack/directory_layout.py
index 4ab9a515cf..ff327ed504 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -53,6 +53,19 @@ 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.
@@ -156,6 +169,11 @@ class SpecHashDirectoryLayout(DirectoryLayout):
         self.extension_file_name = extension_file_name
 
 
+    @property
+    def hidden_file_paths(self):
+        return ('.spec', '.extensions')
+
+
     def relative_path_for_spec(self, spec):
         _check_concrete(spec)
         dir_name = spec.format('$_$@$+$#')
@@ -249,28 +267,32 @@ class SpecHashDirectoryLayout(DirectoryLayout):
 
 
     def get_extensions(self, spec):
-        path = self.extension_file_path(spec)
+        _check_concrete(spec)
 
+        path = self.extension_file_path(spec)
         extensions = set()
         if os.path.exists(path):
-            with closing(open(path)) as spec_file:
-                for line in spec_file:
+            with closing(open(path)) as ext_file:
+                for line in ext_file:
                     try:
-                        extensions.add(Spec(line))
-                    except SpecError, e:
+                        extensions.add(Spec(line.strip()))
+                    except spack.error.SpackError, e:
                         raise InvalidExtensionSpecError(str(e))
         return extensions
 
 
-    def write_extensions(self, extensions):
+    def write_extensions(self, spec, extensions):
         path = self.extension_file_path(spec)
         with closing(open(path, 'w')) as spec_file:
             for extension in sorted(extensions):
-                spec_file.write("%s\n" % extensions)
+                spec_file.write("%s\n" % extension)
 
 
     def add_extension(self, spec, extension_spec):
-        exts = get_extensions(spec)
+        _check_concrete(spec)
+        _check_concrete(extension_spec)
+
+        exts = self.get_extensions(spec)
         if extension_spec in exts:
             raise ExtensionAlreadyInstalledError(spec, extension_spec)
         else:
@@ -279,16 +301,19 @@ class SpecHashDirectoryLayout(DirectoryLayout):
                     raise ExtensionConflictError(spec, extension_spec, already_installed)
 
         exts.add(extension_spec)
-        self.write_extensions(exts)
+        self.write_extensions(spec, exts)
 
 
     def remove_extension(self, spec, extension_spec):
-        exts = get_extensions(spec)
+        _check_concrete(spec)
+        _check_concrete(extension_spec)
+
+        exts = self.get_extensions(spec)
         if not extension_spec in exts:
             raise NoSuchExtensionError(spec, extension_spec)
 
         exts.remove(extension_spec)
-        self.write_extensions(exts)
+        self.write_extensions(spec, exts)
 
 
 class DirectoryLayoutError(SpackError):
@@ -328,7 +353,7 @@ class ExtensionAlreadyInstalledError(DirectoryLayoutError):
     """Raised when an extension is added to a package that already has it."""
     def __init__(self, spec, extension_spec):
         super(ExtensionAlreadyInstalledError, self).__init__(
-            "%s is already installed in %s" % (extension_spec, spec))
+            "%s is already installed in %s" % (extension_spec.short_spec, spec.short_spec))
 
 
 class ExtensionConflictError(DirectoryLayoutError):
@@ -336,12 +361,12 @@ class ExtensionConflictError(DirectoryLayoutError):
     def __init__(self, spec, extension_spec, conflict):
         super(ExtensionConflictError, self).__init__(
             "%s cannot be installed in %s because it conflicts with %s."% (
-                extension_spec, spec, conflict))
+                extension_spec.short_spec, spec.short_spec, conflict.short_spec))
 
 
 class NoSuchExtensionError(DirectoryLayoutError):
     """Raised when an extension isn't there on remove."""
     def __init__(self, spec, extension_spec):
         super(NoSuchExtensionError, self).__init__(
-            "%s cannot be removed from %s beacuse it's not installed."% (
-                extension_spec, spec, conflict))
+            "%s cannot be removed from %s because it's not installed."% (
+                extension_spec.short_spec, spec.short_spec))
diff --git a/lib/spack/spack/hooks/extensions.py b/lib/spack/spack/hooks/extensions.py
new file mode 100644
index 0000000000..444472bffa
--- /dev/null
+++ b/lib/spack/spack/hooks/extensions.py
@@ -0,0 +1,49 @@
+##############################################################################
+# 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 post_install(pkg):
+    assert(pkg.spec.concrete)
+    for name, spec in pkg.extendees.items():
+        ext = pkg.spec[name]
+        epkg = ext.package
+        if epkg.installed:
+            epkg.do_activate(pkg)
+
+
+def pre_uninstall(pkg):
+    assert(pkg.spec.concrete)
+
+    # Need to do this b/c uninstall does not automatically do it.
+    # TODO: store full graph info in stored .spec file.
+    pkg.spec.normalize()
+
+    for name, spec in pkg.extendees.items():
+        ext = pkg.spec[name]
+        epkg = ext.package
+        if epkg.installed:
+            epkg.do_deactivate(pkg)
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 04f0d842da..b7dae552e4 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -329,6 +329,9 @@ class Package(object):
     """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.
@@ -398,6 +401,9 @@ class Package(object):
         self._fetch_time = 0.0
         self._total_time = 0.0
 
+        for name, spec in self.extendees.items():
+            spack.db.get(spec)._check_extendable()
+
 
     @property
     def version(self):
@@ -877,6 +883,79 @@ 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, extension):
+        self._check_extendable()
+        if not self.installed:
+            raise ValueError("Can only (de)activate extensions for installed packages.")
+        if not extension.installed:
+            raise ValueError("Extensions must first be installed.")
+        if not self.name in extension.extendees:
+            raise ValueError("%s does not extend %s!" % (extension.name, self.name))
+        if not self.spec.satisfies(extension.extendees[self.name]):
+            raise ValueError("%s does not satisfy %s!" % (self.spec, extension.spec))
+
+
+    def do_activate(self, extension):
+        self._sanity_check_extension(extension)
+
+        self.activate(extension)
+        spack.install_layout.add_extension(self.spec, extension.spec)
+        tty.msg("Activated extension %s for %s."
+                % (extension.spec.short_spec, self.spec.short_spec))
+
+
+    def activate(self, extension):
+        """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.
+
+        """
+        conflict = check_link_tree(
+            extension.prefix, self.prefix,
+            ignore=spack.install_layout.hidden_file_paths)
+
+        if conflict:
+            raise ExtensionConflictError(conflict)
+
+        merge_link_tree(extension.prefix, self.prefix,
+                        ignore=spack.install_layout.hidden_file_paths)
+
+
+    def do_deactivate(self, extension):
+        self._sanity_check_extension(extension)
+        self.deactivate(extension)
+
+        ext = extension.spec
+        if ext in spack.install_layout.get_extensions(self.spec):
+            spack.install_layout.remove_extension(self.spec, ext)
+
+        tty.msg("Deactivated extension %s for %s."
+                % (extension.spec.short_spec, self.spec.short_spec))
+
+
+    def deactivate(self, extension):
+        """Unlinks all files from extension out of extendee'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.
+
+        """
+        unmerge_link_tree(extension.prefix, self.prefix,
+                          ignore=spack.install_layout.hidden_file_paths)
+        tty.msg("Deactivated %s as extension of %s."
+                % (extension.spec.short_spec, self.spec.short_spec))
+
+
     def do_clean(self):
         if self.stage.expanded_archive_path:
             self.stage.chdir_to_source()
@@ -1068,3 +1147,9 @@ class NoURLError(PackageError):
     def __init__(self, cls):
         super(NoURLError, self).__init__(
             "Package %s has no version with a URL." % cls.__name__)
+
+
+class ExtensionConflictError(PackageError):
+    def __init__(self, path):
+        super(ExtensionConflictError, self).__init__(
+            "Extension blocked by file: %s" % path)
diff --git a/lib/spack/spack/relations.py b/lib/spack/spack/relations.py
index aaca9c199e..17bec1664f 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
@@ -135,7 +135,7 @@ def extends(*specs):
     for string in specs:
         for spec in spack.spec.parse(string):
             if pkg == spec.name:
-                raise CircularReferenceError('depends_on', pkg)
+                raise CircularReferenceError('extends', pkg)
             dependencies[spec.name] = spec
             extendees[spec.name] = spec
 
diff --git a/var/spack/packages/python/package.py b/var/spack/packages/python/package.py
index e6c3e28820..953be69cc2 100644
--- a/var/spack/packages/python/package.py
+++ b/var/spack/packages/python/package.py
@@ -1,10 +1,13 @@
 from spack import *
 
+
 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")
-- 
cgit v1.2.3-70-g09d2


From 82946d29147bbe63855f94b9c2ebd4a21cd0a3d6 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 8 Jan 2015 22:46:31 -0800
Subject: Move symlink tree routines to LinkTree class.

---
 lib/spack/llnl/util/filesystem.py |  82 +------------------
 lib/spack/llnl/util/link_tree.py  | 168 ++++++++++++++++++++++++++++++++++++++
 lib/spack/spack/package.py        |  16 ++--
 3 files changed, 176 insertions(+), 90 deletions(-)
 create mode 100644 lib/spack/llnl/util/link_tree.py

diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index 9fb76d3a35..0578415653 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -24,8 +24,7 @@
 ##############################################################################
 __all__ = ['set_install_permissions', 'install', 'expand_user', 'working_dir',
            'touch', 'mkdirp', 'force_remove', 'join_path', 'ancestor',
-           'can_access', 'filter_file', 'change_sed_delimiter', 'is_exe',
-           'check_link_tree', 'merge_link_tree', 'unmerge_link_tree']
+           'can_access', 'filter_file', 'change_sed_delimiter', 'is_exe']
 
 import os
 import sys
@@ -223,82 +222,3 @@ def ancestor(dir, n=1):
 def can_access(file_name):
     """True if we have read/write access to the file."""
     return os.access(file_name, os.R_OK|os.W_OK)
-
-
-def traverse_link_tree(src_root, dest_root, follow_nonexisting=True, **kwargs):
-    # Yield directories before or after their contents.
-    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', None)
-    if isinstance(ignore, basestring):
-        ignore = (ignore,)
-
-    for dirpath, dirnames, filenames in os.walk(src_root):
-        rel_path  = dirpath[len(src_root):]
-        rel_path = rel_path.lstrip(os.path.sep)
-        dest_dirpath = os.path.join(dest_root, rel_path)
-
-        # Don't descend into ignored directories
-        if ignore and dest_dirpath in ignore:
-            return
-
-        # Don't descend into dirs in dest that do not exist in src.
-        if not follow_nonexisting:
-            dirnames[:] = [
-                d for d in dirnames
-                if os.path.exists(os.path.join(dest_dirpath, d))]
-
-        # preorder yields directories before children
-        if order == 'pre':
-            yield (dirpath, dest_dirpath)
-
-        for name in filenames:
-            src_file  = os.path.join(dirpath, name)
-            dest_file = os.path.join(dest_dirpath, name)
-
-            # Ignore particular paths inside the install root.
-            src_relpath = src_file[len(src_root):]
-            src_relpath = src_relpath.lstrip(os.path.sep)
-            if ignore and src_relpath in ignore:
-                continue
-
-            yield (src_file, dest_file)
-
-        # postorder yields directories after children
-        if order == 'post':
-            yield (dirpath, dest_dirpath)
-
-
-
-def check_link_tree(src_root, dest_root, **kwargs):
-    for src, dest in traverse_link_tree(src_root, dest_root, False, **kwargs):
-        if os.path.exists(dest) and not os.path.isdir(dest):
-            return dest
-    return None
-
-
-def merge_link_tree(src_root, dest_root, **kwargs):
-    kwargs['order'] = 'pre'
-    for src, dest in traverse_link_tree(src_root, dest_root, **kwargs):
-        if os.path.isdir(src):
-            mkdirp(dest)
-        else:
-            assert(not os.path.exists(dest))
-            os.symlink(src, dest)
-
-
-def unmerge_link_tree(src_root, dest_root, **kwargs):
-    kwargs['order'] = 'post'
-    for src, dest in traverse_link_tree(src_root, dest_root, **kwargs):
-        if os.path.isdir(dest):
-            if not os.listdir(dest):
-                # TODO: what if empty directories were present pre-merge?
-                shutil.rmtree(dest, ignore_errors=True)
-
-        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/llnl/util/link_tree.py b/lib/spack/llnl/util/link_tree.py
new file mode 100644
index 0000000000..19c2d46938
--- /dev/null
+++ b/lib/spack/llnl/util/link_tree.py
@@ -0,0 +1,168 @@
+##############################################################################
+# 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 mkdirp
+
+
+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):
+        self._root = source_root
+
+
+    def traverse(self, dest_root, **kwargs):
+        """Traverse LinkTree root and dest 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.  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=<container> -- Optional container of root-relative
+                              paths to ignore.
+
+        follow_nonexisting -- Whether to descend into directories in
+                              src that do not exit in dest.
+
+        """
+        # Yield directories before or after their contents.
+        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', None)
+        if isinstance(ignore, basestring):
+            ignore = (ignore,)
+
+        # Whether to descend when dirs dont' exist in dest.
+        follow_nonexisting = kwargs.get('follow_nonexisting', True)
+
+        for dirpath, dirnames, filenames in os.walk(self._root):
+            rel_path  = dirpath[len(self._root):]
+            rel_path = rel_path.lstrip(os.path.sep)
+            dest_dirpath = os.path.join(dest_root, rel_path)
+
+            # Don't descend into ignored directories
+            if ignore and dest_dirpath in ignore:
+                return
+
+            # Don't descend into dirs in dest that do not exist in src.
+            if not follow_nonexisting:
+                dirnames[:] = [
+                    d for d in dirnames
+                    if os.path.exists(os.path.join(dest_dirpath, d))]
+
+            # preorder yields directories before children
+            if order == 'pre':
+                yield (dirpath, dest_dirpath)
+
+            for name in filenames:
+                src_file  = os.path.join(dirpath, name)
+                dest_file = os.path.join(dest_dirpath, name)
+
+                # Ignore particular paths inside the install root.
+                src_relpath = src_file[len(self._root):]
+                src_relpath = src_relpath.lstrip(os.path.sep)
+                if ignore and src_relpath in ignore:
+                    continue
+
+                yield (src_file, dest_file)
+
+            # postorder yields directories after children
+            if order == 'post':
+                yield (dirpath, dest_dirpath)
+
+
+
+    def find_conflict(self, dest_root, **kwargs):
+        """Returns the first file in dest that also exists in src."""
+        kwargs['follow_nonexisting'] = False
+        for src, dest in self.traverse(dest_root, **kwargs):
+            if os.path.exists(dest) and not os.path.isdir(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 self.traverse(dest_root, **kwargs):
+            if os.path.isdir(src):
+                mkdirp(dest)
+            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 self.traverse(dest_root, **kwargs):
+            if os.path.isdir(dest):
+                if not os.listdir(dest):
+                    # TODO: what if empty directories were present pre-merge?
+                    shutil.rmtree(dest, ignore_errors=True)
+
+            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/package.py b/lib/spack/spack/package.py
index b7dae552e4..da251dc4e8 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 *
 
@@ -918,15 +919,12 @@ class Package(object):
         always executed.
 
         """
-        conflict = check_link_tree(
-            extension.prefix, self.prefix,
-            ignore=spack.install_layout.hidden_file_paths)
-
+        tree = LinkTree(extension.prefix)
+        conflict = tree.find_conflict(
+            self.prefix, ignore=spack.install_layout.hidden_file_paths)
         if conflict:
             raise ExtensionConflictError(conflict)
-
-        merge_link_tree(extension.prefix, self.prefix,
-                        ignore=spack.install_layout.hidden_file_paths)
+        tree.merge(self.prefix, ignore=spack.install_layout.hidden_file_paths)
 
 
     def do_deactivate(self, extension):
@@ -950,8 +948,8 @@ class Package(object):
         always executed.
 
         """
-        unmerge_link_tree(extension.prefix, self.prefix,
-                          ignore=spack.install_layout.hidden_file_paths)
+        tree = LinkTree(extension.prefix)
+        tree.unmerge(self.prefix, ignore=spack.install_layout.hidden_file_paths)
         tty.msg("Deactivated %s as extension of %s."
                 % (extension.spec.short_spec, self.spec.short_spec))
 
-- 
cgit v1.2.3-70-g09d2


From bcccf020204a556e382c0af2897ad9126bb24984 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 10 Jan 2015 19:37:01 -0800
Subject: Add setup_extension_environment() method.

- lets packages do some setup before their extensions run install()
---
 lib/spack/spack/package.py                  | 30 +++++++++++++++++++++++++++++
 var/spack/packages/py-setuptools/package.py |  6 ------
 var/spack/packages/python/package.py        | 23 +++++++++++++++++++++-
 3 files changed, 52 insertions(+), 7 deletions(-)

diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index da251dc4e8..8504b96fcf 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -783,6 +783,12 @@ class Package(object):
                 self.stage.chdir_to_source()
                 build_env.setup_package(self)
 
+                # Allow extendees to further set up the environment.
+                for ext_name in self.extendees:
+                    ext_spec = self.spec[ext_name]
+                    ext_spec.package.setup_extension_environment(
+                        self.module, ext_spec, self.spec)
+
                 if fake_install:
                     self.do_fake_install()
                 else:
@@ -854,6 +860,30 @@ class Package(object):
                           fromlist=[self.__class__.__name__])
 
 
+    def setup_extension_environment(self, module, spec, ext_spec):
+        """Called before the install() method of extensions.
+
+        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.
+
+        """
+        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)
diff --git a/var/spack/packages/py-setuptools/package.py b/var/spack/packages/py-setuptools/package.py
index e2c4e1a0be..755288d55c 100644
--- a/var/spack/packages/py-setuptools/package.py
+++ b/var/spack/packages/py-setuptools/package.py
@@ -10,10 +10,4 @@ class PySetuptools(Package):
     extends('python')
 
     def install(self, spec, prefix):
-        site_packages_dir = "%s/lib/python2.7/site-packages" % prefix
-        mkdirp(site_packages_dir)
-
-        env['PYTHONPATH'] = site_packages_dir
-
-        python = which('python')
         python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/python/package.py b/var/spack/packages/python/package.py
index 953be69cc2..9700179ab8 100644
--- a/var/spack/packages/python/package.py
+++ b/var/spack/packages/python/package.py
@@ -1,5 +1,5 @@
 from spack import *
-
+import os
 
 class Python(Package):
     """The Python programming language."""
@@ -26,3 +26,24 @@ class Python(Package):
                   "--enable-shared")
         make()
         make("install")
+
+
+    def setup_extension_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 = join_path(ext_spec.prefix.lib, 'python%d.%d' % self.version[:2])
+        module.site_packages_dir = join_path(module.python_lib_dir, 'site-packages')
+
+        # Add site packages directory to the PYTHONPATH
+        os.environ['PYTHONPATH'] = module.site_packages_dir
+
+        # Make the site packages directory if it does not exist already.
+        mkdirp(module.site_packages_dir)
-- 
cgit v1.2.3-70-g09d2


From d13bbeb605f56214db919f6f122a8fa6ba67ddbc Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 10 Jan 2015 19:52:07 -0800
Subject: Add PYTOHNPATH to modules for python extensions.

---
 lib/spack/spack/modules.py | 8 ++++++++
 1 file changed, 8 insertions(+)

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("$_ $@")
-- 
cgit v1.2.3-70-g09d2


From acc62abbd08f6d44c930b0ceed74fb9e47f365cf Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 12 Jan 2015 22:39:18 -0800
Subject: Rework do_activate/activate and do_deactivate/deactivate semantics.

- packages can now extend only one other package.
- do_activate() and do_deactivate() are now called on the extension,
  and they automatically find the extendee
- activate() and deactivate() are still called on the extendee and are
  passed the extension.
---
 lib/spack/spack/cmd/__init__.py     | 15 ++++++
 lib/spack/spack/cmd/location.py     | 47 ++++++++----------
 lib/spack/spack/cmd/uninstall.py    |  1 -
 lib/spack/spack/hooks/extensions.py | 15 +-----
 lib/spack/spack/package.py          | 97 ++++++++++++++++++++++++-------------
 lib/spack/spack/packages.py         |  2 +
 lib/spack/spack/relations.py        |  2 +
 7 files changed, 105 insertions(+), 74 deletions(-)

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/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/hooks/extensions.py b/lib/spack/spack/hooks/extensions.py
index 444472bffa..2cf506beed 100644
--- a/lib/spack/spack/hooks/extensions.py
+++ b/lib/spack/spack/hooks/extensions.py
@@ -27,23 +27,12 @@ import spack
 
 
 def post_install(pkg):
-    assert(pkg.spec.concrete)
-    for name, spec in pkg.extendees.items():
-        ext = pkg.spec[name]
-        epkg = ext.package
-        if epkg.installed:
-            epkg.do_activate(pkg)
+    pkg.do_activate()
 
 
 def pre_uninstall(pkg):
-    assert(pkg.spec.concrete)
-
     # Need to do this b/c uninstall does not automatically do it.
     # TODO: store full graph info in stored .spec file.
     pkg.spec.normalize()
 
-    for name, spec in pkg.extendees.items():
-        ext = pkg.spec[name]
-        epkg = ext.package
-        if epkg.installed:
-            epkg.do_deactivate(pkg)
+    pkg.do_deactivate()
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 8504b96fcf..ae34f8ae45 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -315,15 +315,18 @@ class Package(object):
     """Specs of virtual packages provided by this package, keyed by name."""
     provided = {}
 
-    """Specs of packages this one extends, keyed by name."""
-    extendees = {}
-
     """Specs of conflicting packages, keyed by name. """
     conflicted = {}
 
     """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.
     #
@@ -402,8 +405,8 @@ class Package(object):
         self._fetch_time = 0.0
         self._total_time = 0.0
 
-        for name, spec in self.extendees.items():
-            spack.db.get(spec)._check_extendable()
+        if self.is_extension:
+            spack.db.get(self.extendee_spec)._check_extendable()
 
 
     @property
@@ -491,6 +494,34 @@ 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:
+            return self.extendees[name]
+
+        # Need to do this to get the concrete version of the spec
+        return self.spec[name]
+
+
+    @property
+    def is_extension(self):
+        return len(self.extendees) > 0
+
+
+    @property
+    def activated(self):
+        if not self.spec.concrete:
+            raise ValueError("Only concrete package extensions can be activated.")
+        if not self.is_extension:
+            raise ValueError("is_extension called on package that is not an extension.")
+
+        return self.spec in spack.install_layout.get_extensions(self.extendee_spec)
+
+
     def preorder_traversal(self, visited=None, **kwargs):
         """This does a preorder traversal of the package's dependence DAG."""
         virtual = kwargs.get("virtual", False)
@@ -784,10 +815,9 @@ class Package(object):
                 build_env.setup_package(self)
 
                 # Allow extendees to further set up the environment.
-                for ext_name in self.extendees:
-                    ext_spec = self.spec[ext_name]
-                    ext_spec.package.setup_extension_environment(
-                        self.module, ext_spec, self.spec)
+                if self.is_extension:
+                    self.extendee_spec.package.setup_extension_environment(
+                        self.module, self.extendee_spec, self.spec)
 
                 if fake_install:
                     self.do_fake_install()
@@ -840,7 +870,6 @@ class Package(object):
         if returncode != 0:
             sys.exit(1)
 
-
         # Once everything else is done, run post install hooks
         spack.hooks.post_install(self)
 
@@ -919,25 +948,30 @@ class Package(object):
             raise ValueError("Package %s is not extendable!" % self.name)
 
 
-    def _sanity_check_extension(self, extension):
-        self._check_extendable()
-        if not self.installed:
+    def _sanity_check_extension(self):
+        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 extension.installed:
+        if not self.installed:
             raise ValueError("Extensions must first be installed.")
-        if not self.name in extension.extendees:
-            raise ValueError("%s does not extend %s!" % (extension.name, self.name))
-        if not self.spec.satisfies(extension.extendees[self.name]):
-            raise ValueError("%s does not satisfy %s!" % (self.spec, extension.spec))
+        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):
+        """Called on an etension to invoke the extendee's activate method.
 
-    def do_activate(self, extension):
-        self._sanity_check_extension(extension)
+        Commands should call this routine, and should not call
+        activate() directly.
+        """
+        self._sanity_check_extension()
+        self.extendee_spec.package.activate(self)
 
-        self.activate(extension)
-        spack.install_layout.add_extension(self.spec, extension.spec)
+        spack.install_layout.add_extension(self.extendee_spec, self.spec)
         tty.msg("Activated extension %s for %s."
-                % (extension.spec.short_spec, self.spec.short_spec))
+                % (self.spec.short_spec, self.extendee_spec.short_spec))
 
 
     def activate(self, extension):
@@ -957,20 +991,19 @@ class Package(object):
         tree.merge(self.prefix, ignore=spack.install_layout.hidden_file_paths)
 
 
-    def do_deactivate(self, extension):
-        self._sanity_check_extension(extension)
-        self.deactivate(extension)
+    def do_deactivate(self):
+        self._sanity_check_extension()
+        self.extendee_spec.package.deactivate(self)
 
-        ext = extension.spec
-        if ext in spack.install_layout.get_extensions(self.spec):
-            spack.install_layout.remove_extension(self.spec, ext)
+        if self.spec in spack.install_layout.get_extensions(self.extendee_spec):
+            spack.install_layout.remove_extension(self.extendee_spec, self.spec)
 
         tty.msg("Deactivated extension %s for %s."
-                % (extension.spec.short_spec, self.spec.short_spec))
+                % (self.spec.short_spec, self.extendee_spec.short_spec))
 
 
     def deactivate(self, extension):
-        """Unlinks all files from extension out of extendee's install dir.
+        """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.)
@@ -980,8 +1013,6 @@ class Package(object):
         """
         tree = LinkTree(extension.prefix)
         tree.unmerge(self.prefix, ignore=spack.install_layout.hidden_file_paths)
-        tty.msg("Deactivated %s as extension of %s."
-                % (extension.spec.short_spec, self.spec.short_spec))
 
 
     def do_clean(self):
diff --git a/lib/spack/spack/packages.py b/lib/spack/spack/packages.py
index db43d3909a..bb5a94bcab 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]
diff --git a/lib/spack/spack/relations.py b/lib/spack/spack/relations.py
index 17bec1664f..60ff5bef34 100644
--- a/lib/spack/spack/relations.py
+++ b/lib/spack/spack/relations.py
@@ -131,6 +131,8 @@ def extends(*specs):
     clocals = caller_locals()
     dependencies = clocals.setdefault('dependencies', {})
     extendees = clocals.setdefault('extendees', {})
+    if extendees:
+        raise RelationError("Packages can extend at most one other package.")
 
     for string in specs:
         for spec in spack.spec.parse(string):
-- 
cgit v1.2.3-70-g09d2


From 89ccdf92cd42a52fa42d39e2be580eac110e264a Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 12 Jan 2015 22:41:27 -0800
Subject: Add activate and deactivate commands for extensions.

---
 lib/spack/spack/cmd/activate.py   | 50 +++++++++++++++++++++++++++++++++++++++
 lib/spack/spack/cmd/deactivate.py | 50 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 100 insertions(+)
 create mode 100644 lib/spack/spack/cmd/activate.py
 create mode 100644 lib/spack/spack/cmd/deactivate.py

diff --git a/lib/spack/spack/cmd/activate.py b/lib/spack/spack/cmd/activate.py
new file mode 100644
index 0000000000..c1e23852d6
--- /dev/null
+++ b/lib/spack/spack/cmd/activate.py
@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by 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(
+        '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 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/deactivate.py b/lib/spack/spack/cmd/deactivate.py
new file mode 100644
index 0000000000..fd13f051df
--- /dev/null
+++ b/lib/spack/spack/cmd/deactivate.py
@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by 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 = "Deactivate a package extension."
+
+def setup_parser(subparser):
+    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 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.activated:
+        tty.die("Package %s is not activated." % specs[0].short_spec)
+
+    spec.package.do_deactivate()
-- 
cgit v1.2.3-70-g09d2


From 2ae7f53b8359841fc5d1d7b6c70ff72f38bf2d88 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 15 Jan 2015 09:33:51 -0800
Subject: Bugfix: Extension hooks shoudl only run for extensions.

---
 lib/spack/spack/hooks/extensions.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/hooks/extensions.py b/lib/spack/spack/hooks/extensions.py
index 2cf506beed..718b24b965 100644
--- a/lib/spack/spack/hooks/extensions.py
+++ b/lib/spack/spack/hooks/extensions.py
@@ -27,7 +27,8 @@ import spack
 
 
 def post_install(pkg):
-    pkg.do_activate()
+    if pkg.is_extension:
+        pkg.do_activate()
 
 
 def pre_uninstall(pkg):
@@ -35,4 +36,5 @@ def pre_uninstall(pkg):
     # TODO: store full graph info in stored .spec file.
     pkg.spec.normalize()
 
-    pkg.do_deactivate()
+    if pkg.is_extension:
+        pkg.do_deactivate()
-- 
cgit v1.2.3-70-g09d2


From 7992f415fe0e50c5e15964f348ed23c1fc1795b5 Mon Sep 17 00:00:00 2001
From: "Gregory L. Lee" <lee218@llnl.gov>
Date: Thu, 15 Jan 2015 10:11:40 -0800
Subject: added py-nose

---
 var/spack/packages/py-nose/package.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 var/spack/packages/py-nose/package.py

diff --git a/var/spack/packages/py-nose/package.py b/var/spack/packages/py-nose/package.py
new file mode 100644
index 0000000000..7bd7106b8c
--- /dev/null
+++ b/var/spack/packages/py-nose/package.py
@@ -0,0 +1,13 @@
+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')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
-- 
cgit v1.2.3-70-g09d2


From 9fa489b7f2dab452929729e300f189f8c50b817c Mon Sep 17 00:00:00 2001
From: "Gregory L. Lee" <lee218@llnl.gov>
Date: Tue, 20 Jan 2015 09:39:21 -0800
Subject: added several modules

---
 var/spack/packages/py-cython/package.py     | 13 +++++++++++++
 var/spack/packages/py-dateutil/package.py   | 13 +++++++++++++
 var/spack/packages/py-epydoc/package.py     | 13 +++++++++++++
 var/spack/packages/py-ipython/package.py    | 14 ++++++++++++++
 var/spack/packages/py-matplotlib/package.py | 20 ++++++++++++++++++++
 var/spack/packages/py-numpy/package.py      | 14 ++++++++++++++
 var/spack/packages/py-pexpect/package.py    | 13 +++++++++++++
 var/spack/packages/py-pygments/package.py   | 14 ++++++++++++++
 var/spack/packages/py-pyparsing/package.py  | 13 +++++++++++++
 var/spack/packages/py-pyside/package.py     | 18 ++++++++++++++++++
 var/spack/packages/py-pytz/package.py       | 13 +++++++++++++
 var/spack/packages/py-scipy/package.py      | 15 +++++++++++++++
 var/spack/packages/py-six/package.py        | 13 +++++++++++++
 var/spack/packages/py-virtualenv/package.py | 18 ++++++++++++++++++
 14 files changed, 204 insertions(+)
 create mode 100644 var/spack/packages/py-cython/package.py
 create mode 100644 var/spack/packages/py-dateutil/package.py
 create mode 100644 var/spack/packages/py-epydoc/package.py
 create mode 100644 var/spack/packages/py-ipython/package.py
 create mode 100644 var/spack/packages/py-matplotlib/package.py
 create mode 100644 var/spack/packages/py-numpy/package.py
 create mode 100644 var/spack/packages/py-pexpect/package.py
 create mode 100644 var/spack/packages/py-pygments/package.py
 create mode 100644 var/spack/packages/py-pyparsing/package.py
 create mode 100644 var/spack/packages/py-pyside/package.py
 create mode 100644 var/spack/packages/py-pytz/package.py
 create mode 100644 var/spack/packages/py-scipy/package.py
 create mode 100644 var/spack/packages/py-six/package.py
 create mode 100644 var/spack/packages/py-virtualenv/package.py

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..96e3ecab07
--- /dev/null
+++ b/var/spack/packages/py-dateutil/package.py
@@ -0,0 +1,13 @@
+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')
+
+    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-ipython/package.py b/var/spack/packages/py-ipython/package.py
new file mode 100644
index 0000000000..731e661dfd
--- /dev/null
+++ b/var/spack/packages/py-ipython/package.py
@@ -0,0 +1,14 @@
+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')
+
+    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..836273c923
--- /dev/null
+++ b/var/spack/packages/py-matplotlib/package.py
@@ -0,0 +1,20 @@
+from spack import *
+
+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')
+    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')
+
+    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-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-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-pyside/package.py b/var/spack/packages/py-pyside/package.py
new file mode 100644
index 0000000000..b01e16d7e6
--- /dev/null
+++ b/var/spack/packages/py-pyside/package.py
@@ -0,0 +1,18 @@
+from spack import *
+import spack.package
+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')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        qmake_path = '/usr/lib64/qt4/bin/qmake'
+        if not os.path.exists(qmake_path):
+            raise spack.package.InstallError("Failed to find qmake in %s" % qmake_path)
+        python('setup.py', 'install', '--prefix=%s' % prefix, '--qmake=%s' % qmake_path)
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-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-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-virtualenv/package.py b/var/spack/packages/py-virtualenv/package.py
new file mode 100644
index 0000000000..c1b359e164
--- /dev/null
+++ b/var/spack/packages/py-virtualenv/package.py
@@ -0,0 +1,18 @@
+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')
+
+    def clean(self):
+        if os.path.exists('build'):
+            shutil.rmtree('build')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
-- 
cgit v1.2.3-70-g09d2


From ff9cb94f4f92112739f53881bcb0a9a19811684d Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 20 Jan 2015 00:23:16 -0800
Subject: Add arguements to extends() and activate/deactivate.

---
 lib/spack/spack/package.py           | 40 ++++++++++++++++++++++++++----------
 lib/spack/spack/relations.py         | 17 ++++++++-------
 var/spack/packages/python/package.py | 32 +++++++++++++++++++++++++++--
 3 files changed, 69 insertions(+), 20 deletions(-)

diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index ae34f8ae45..bd63c2e0c0 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -497,16 +497,26 @@ class Package(object):
     @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
-
+        if not self.extendees:
+            return None
         name = next(iter(self.extendees))
         if not name in self.spec:
-            return self.extendees[name]
+            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
@@ -949,6 +959,8 @@ class Package(object):
 
 
     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()
 
@@ -967,14 +979,14 @@ class Package(object):
         activate() directly.
         """
         self._sanity_check_extension()
-        self.extendee_spec.package.activate(self)
+        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.short_spec))
 
 
-    def activate(self, extension):
+    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
@@ -983,17 +995,20 @@ class Package(object):
         always executed.
 
         """
+        ignore_files = set(spack.install_layout.hidden_file_paths)
+        ignore_files.update(kwargs.get('ignore', ()))
+
         tree = LinkTree(extension.prefix)
-        conflict = tree.find_conflict(
-            self.prefix, ignore=spack.install_layout.hidden_file_paths)
+        conflict = tree.find_conflict(self.prefix, ignore=ignore_files)
         if conflict:
             raise ExtensionConflictError(conflict)
-        tree.merge(self.prefix, ignore=spack.install_layout.hidden_file_paths)
+        tree.merge(self.prefix, ignore=ignore_files)
 
 
     def do_deactivate(self):
+        """Called on the extension to invoke extendee's deactivate() method."""
         self._sanity_check_extension()
-        self.extendee_spec.package.deactivate(self)
+        self.extendee_spec.package.deactivate(self, **self.extendee_args)
 
         if self.spec in spack.install_layout.get_extensions(self.extendee_spec):
             spack.install_layout.remove_extension(self.extendee_spec, self.spec)
@@ -1002,7 +1017,7 @@ class Package(object):
                 % (self.spec.short_spec, self.extendee_spec.short_spec))
 
 
-    def deactivate(self, extension):
+    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
@@ -1011,8 +1026,11 @@ class Package(object):
         always executed.
 
         """
+        ignore_files = set(spack.install_layout.hidden_file_paths)
+        ignore_files.update(kwargs.get('ignore', ()))
+
         tree = LinkTree(extension.prefix)
-        tree.unmerge(self.prefix, ignore=spack.install_layout.hidden_file_paths)
+        tree.unmerge(self.prefix, ignore=ignore_files)
 
 
     def do_clean(self):
diff --git a/lib/spack/spack/relations.py b/lib/spack/spack/relations.py
index 60ff5bef34..a0c7723473 100644
--- a/lib/spack/spack/relations.py
+++ b/lib/spack/spack/relations.py
@@ -117,7 +117,7 @@ def depends_on(*specs):
             dependencies[spec.name] = spec
 
 
-def extends(*specs):
+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
@@ -126,6 +126,10 @@ def extends(*specs):
     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()
@@ -134,12 +138,11 @@ def extends(*specs):
     if extendees:
         raise RelationError("Packages can extend at most one other package.")
 
-    for string in specs:
-        for spec in spack.spec.parse(string):
-            if pkg == spec.name:
-                raise CircularReferenceError('extends', pkg)
-            dependencies[spec.name] = spec
-            extendees[spec.name] = spec
+    spec = Spec(spec)
+    if pkg == spec.name:
+        raise CircularReferenceError('extends', pkg)
+    dependencies[spec.name] = spec
+    extendees[spec.name] = (spec, kwargs)
 
 
 def provides(*specs, **kwargs):
diff --git a/var/spack/packages/python/package.py b/var/spack/packages/python/package.py
index 9700179ab8..86b903bc23 100644
--- a/var/spack/packages/python/package.py
+++ b/var/spack/packages/python/package.py
@@ -28,6 +28,16 @@ class Python(Package):
         make("install")
 
 
+    @property
+    def python_lib_dir(self):
+        return os.path.join('lib', 'python%d.%d' % self.version[:2])
+
+
+    @property
+    def site_packages_dir(self):
+        return os.path.join(self.python_lib_dir, 'site-packages')
+
+
     def setup_extension_environment(self, module, spec, ext_spec):
         """Called before python modules' install() methods.
 
@@ -39,11 +49,29 @@ class Python(Package):
         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 = join_path(ext_spec.prefix.lib, 'python%d.%d' % self.version[:2])
-        module.site_packages_dir = join_path(module.python_lib_dir, 'site-packages')
+        module.python_lib_dir = os.path.join(ext_spec.prefix, self.python_lib_dir)
+        module.site_packages_dir = os.path.join(ext_spec.prefix, self.site_packages_dir)
 
         # Add site packages directory to the PYTHONPATH
         os.environ['PYTHONPATH'] = module.site_packages_dir
 
         # Make the site packages directory if it does not exist already.
         mkdirp(module.site_packages_dir)
+
+
+    def add_ignore_files(self, args):
+        """Add some ignore files to activate/deactivate args."""
+        ignore  = set(args.get('ignore', ()))
+        ignore.add(os.path.join(self.site_packages_dir, 'site.py'))
+        ignore.add(os.path.join(self.site_packages_dir, 'site.pyc'))
+        args.update(ignore=ignore)
+
+
+    def activate(self, ext_pkg, **args):
+        self.add_ignore_files(args)
+        super(Python, self).activate(ext_pkg, **args)
+
+
+    def deactivate(self, ext_pkg, **args):
+        self.add_ignore_files(args)
+        super(Python, self).deactivate(ext_pkg, **args)
-- 
cgit v1.2.3-70-g09d2


From de91c95e8e45b8ab066ba3dfc8f89c92da761b5a Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 20 Jan 2015 15:07:53 -0800
Subject: Ability to ignore files in activate/deactivate for extensions.

---
 lib/spack/llnl/util/link_tree.py      | 11 ++++-------
 lib/spack/spack/package.py            | 16 +++++++++-------
 var/spack/packages/py-nose/package.py |  4 +++-
 var/spack/packages/python/package.py  | 17 ++++++++++-------
 4 files changed, 26 insertions(+), 22 deletions(-)

diff --git a/lib/spack/llnl/util/link_tree.py b/lib/spack/llnl/util/link_tree.py
index 19c2d46938..2d7126be2c 100644
--- a/lib/spack/llnl/util/link_tree.py
+++ b/lib/spack/llnl/util/link_tree.py
@@ -72,8 +72,7 @@ class LinkTree(object):
 
         order=[pre|post] -- Whether to do pre- or post-order traveral.
 
-        ignore=<container> -- Optional container of root-relative
-                              paths to ignore.
+        ignore=<predicate> -- Predicate indicating which files to ignore.
 
         follow_nonexisting -- Whether to descend into directories in
                               src that do not exit in dest.
@@ -85,9 +84,7 @@ class LinkTree(object):
             raise ValueError("Order must be 'pre' or 'post'.")
 
         # List of relative paths to ignore under the src root.
-        ignore = kwargs.get('ignore', None)
-        if isinstance(ignore, basestring):
-            ignore = (ignore,)
+        ignore = kwargs.get('ignore', lambda filename: False)
 
         # Whether to descend when dirs dont' exist in dest.
         follow_nonexisting = kwargs.get('follow_nonexisting', True)
@@ -98,7 +95,7 @@ class LinkTree(object):
             dest_dirpath = os.path.join(dest_root, rel_path)
 
             # Don't descend into ignored directories
-            if ignore and dest_dirpath in ignore:
+            if ignore(dest_dirpath):
                 return
 
             # Don't descend into dirs in dest that do not exist in src.
@@ -118,7 +115,7 @@ class LinkTree(object):
                 # Ignore particular paths inside the install root.
                 src_relpath = src_file[len(self._root):]
                 src_relpath = src_relpath.lstrip(os.path.sep)
-                if ignore and src_relpath in ignore:
+                if ignore(src_relpath):
                     continue
 
                 yield (src_file, dest_file)
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index bd63c2e0c0..43b1fcd9c8 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -995,14 +995,15 @@ class Package(object):
         always executed.
 
         """
-        ignore_files = set(spack.install_layout.hidden_file_paths)
-        ignore_files.update(kwargs.get('ignore', ()))
+        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_files)
+        conflict = tree.find_conflict(self.prefix, ignore=ignore)
         if conflict:
             raise ExtensionConflictError(conflict)
-        tree.merge(self.prefix, ignore=ignore_files)
+        tree.merge(self.prefix, ignore=ignore)
 
 
     def do_deactivate(self):
@@ -1026,11 +1027,12 @@ class Package(object):
         always executed.
 
         """
-        ignore_files = set(spack.install_layout.hidden_file_paths)
-        ignore_files.update(kwargs.get('ignore', ()))
+        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_files)
+        tree.unmerge(self.prefix, ignore=ignore)
 
 
     def do_clean(self):
diff --git a/var/spack/packages/py-nose/package.py b/var/spack/packages/py-nose/package.py
index 7bd7106b8c..6df84e831d 100644
--- a/var/spack/packages/py-nose/package.py
+++ b/var/spack/packages/py-nose/package.py
@@ -1,7 +1,9 @@
 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."""
+    """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"
 
diff --git a/var/spack/packages/python/package.py b/var/spack/packages/python/package.py
index 86b903bc23..a22bd54c82 100644
--- a/var/spack/packages/python/package.py
+++ b/var/spack/packages/python/package.py
@@ -1,5 +1,6 @@
 from spack import *
 import os
+import re
 
 class Python(Package):
     """The Python programming language."""
@@ -59,19 +60,21 @@ class Python(Package):
         mkdirp(module.site_packages_dir)
 
 
-    def add_ignore_files(self, args):
+    def make_ignore(self, args):
         """Add some ignore files to activate/deactivate args."""
-        ignore  = set(args.get('ignore', ()))
-        ignore.add(os.path.join(self.site_packages_dir, 'site.py'))
-        ignore.add(os.path.join(self.site_packages_dir, 'site.pyc'))
-        args.update(ignore=ignore)
+        orig_ignore = args.get('ignore', lambda f: False)
+        def ignore(filename):
+            return (re.search(r'/site\.pyc?$', filename) or
+                    re.search(r'\.pth$', filename) or
+                    orig_ignore(filename))
+        return ignore
 
 
     def activate(self, ext_pkg, **args):
-        self.add_ignore_files(args)
+        args.update(ignore=self.make_ignore(args))
         super(Python, self).activate(ext_pkg, **args)
 
 
     def deactivate(self, ext_pkg, **args):
-        self.add_ignore_files(args)
+        args.update(ignore=self.make_ignore(args))
         super(Python, self).deactivate(ext_pkg, **args)
-- 
cgit v1.2.3-70-g09d2


From 2bc3f74df263eb92a99e5477f4ce04972eb76994 Mon Sep 17 00:00:00 2001
From: "Gregory L. Lee" <lee218@llnl.gov>
Date: Thu, 22 Jan 2015 11:50:01 -0800
Subject: added more Python modules

---
 var/spack/packages/hdf5/package.py                |  6 ++++--
 var/spack/packages/py-basemap/package.py          | 24 +++++++++++++++++++++++
 var/spack/packages/py-biopython/package.py        | 14 +++++++++++++
 var/spack/packages/py-gnuplot/package.py          | 13 ++++++++++++
 var/spack/packages/py-h5py/package.py             | 18 +++++++++++++++++
 var/spack/packages/py-matplotlib/package.py       | 17 ++++++++++++++++
 var/spack/packages/py-mpi4py/package.py           | 13 ++++++++++++
 var/spack/packages/py-mx/package.py               | 13 ++++++++++++
 var/spack/packages/py-pil/package.py              | 14 +++++++++++++
 var/spack/packages/py-pmw/package.py              | 13 ++++++++++++
 var/spack/packages/py-pylint/package.py           | 16 +++++++++++++++
 var/spack/packages/py-rpy2/package.py             | 14 +++++++++++++
 var/spack/packages/py-scientificpython/package.py | 13 ++++++++++++
 var/spack/packages/py-scikit-learn/package.py     | 13 ++++++++++++
 var/spack/packages/py-sympy/package.py            | 13 ++++++++++++
 15 files changed, 212 insertions(+), 2 deletions(-)
 create mode 100644 var/spack/packages/py-basemap/package.py
 create mode 100644 var/spack/packages/py-biopython/package.py
 create mode 100644 var/spack/packages/py-gnuplot/package.py
 create mode 100644 var/spack/packages/py-h5py/package.py
 create mode 100644 var/spack/packages/py-mpi4py/package.py
 create mode 100644 var/spack/packages/py-mx/package.py
 create mode 100644 var/spack/packages/py-pil/package.py
 create mode 100644 var/spack/packages/py-pmw/package.py
 create mode 100644 var/spack/packages/py-pylint/package.py
 create mode 100644 var/spack/packages/py-rpy2/package.py
 create mode 100644 var/spack/packages/py-scientificpython/package.py
 create mode 100644 var/spack/packages/py-scikit-learn/package.py
 create mode 100644 var/spack/packages/py-sympy/package.py

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/py-basemap/package.py b/var/spack/packages/py-basemap/package.py
new file mode 100644
index 0000000000..8955bf8827
--- /dev/null
+++ b/var/spack/packages/py-basemap/package.py
@@ -0,0 +1,24 @@
+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')
+
+    geos_version = {'1.0.7' : '3.3.3'}
+
+    extends('python')
+    depends_on('py-numpy')
+    depends_on('py-matplotlib')
+    depends_on('py-pil')
+
+    def install(self, spec, prefix):
+        with working_dir('geos-%s' % self.geos_version[str(self.version)]):
+            configure("--prefix=" + prefix)
+            make()
+            make("install")
+        os.environ['GEOS_DIR'] = 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..2ed04c389e
--- /dev/null
+++ b/var/spack/packages/py-biopython/package.py
@@ -0,0 +1,14 @@
+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')
+
+    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..0a2c073a49
--- /dev/null
+++ b/var/spack/packages/py-gnuplot/package.py
@@ -0,0 +1,13 @@
+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')
+
+    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-matplotlib/package.py b/var/spack/packages/py-matplotlib/package.py
index 836273c923..270a1ebfe4 100644
--- a/var/spack/packages/py-matplotlib/package.py
+++ b/var/spack/packages/py-matplotlib/package.py
@@ -1,4 +1,5 @@
 from spack import *
+import os
 
 class PyMatplotlib(Package):
     """Python plotting package."""
@@ -18,3 +19,19 @@ class PyMatplotlib(Package):
 
     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..fdea340dc2
--- /dev/null
+++ b/var/spack/packages/py-mpi4py/package.py
@@ -0,0 +1,13 @@
+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('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-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-pylint/package.py b/var/spack/packages/py-pylint/package.py
new file mode 100644
index 0000000000..ebde861f94
--- /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')
+    extends('python', ignore=lambda f:re.match(r"site.py*", f))
+    depends_on('py-nose')
+
+    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..3817059911
--- /dev/null
+++ b/var/spack/packages/py-rpy2/package.py
@@ -0,0 +1,14 @@
+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')
+
+    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..73600e6cb9
--- /dev/null
+++ b/var/spack/packages/py-scientificpython/package.py
@@ -0,0 +1,13 @@
+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-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)
-- 
cgit v1.2.3-70-g09d2


From 48f1ff87f836f214e72e1d02f47eac4678f0292a Mon Sep 17 00:00:00 2001
From: "Gregory L. Lee" <lee218@llnl.gov>
Date: Fri, 23 Jan 2015 13:53:36 -0800
Subject: added more Python modules

---
 var/spack/packages/py-dateutil/package.py   |  1 +
 var/spack/packages/py-libxml2/package.py    | 13 +++++++++++++
 var/spack/packages/py-matplotlib/package.py |  1 +
 var/spack/packages/py-pychecker/package.py  | 13 +++++++++++++
 var/spack/packages/py-pyqt4/package.py      | 18 ++++++++++++++++++
 var/spack/packages/py-sip/package.py        | 15 +++++++++++++++
 var/spack/packages/qt/package.py            |  5 +++--
 7 files changed, 64 insertions(+), 2 deletions(-)
 create mode 100644 var/spack/packages/py-libxml2/package.py
 create mode 100644 var/spack/packages/py-pychecker/package.py
 create mode 100644 var/spack/packages/py-pyqt4/package.py
 create mode 100644 var/spack/packages/py-sip/package.py

diff --git a/var/spack/packages/py-dateutil/package.py b/var/spack/packages/py-dateutil/package.py
index 96e3ecab07..11699e07ee 100644
--- a/var/spack/packages/py-dateutil/package.py
+++ b/var/spack/packages/py-dateutil/package.py
@@ -8,6 +8,7 @@ class PyDateutil(Package):
     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-libxml2/package.py b/var/spack/packages/py-libxml2/package.py
new file mode 100644
index 0000000000..0dcefbd9cf
--- /dev/null
+++ b/var/spack/packages/py-libxml2/package.py
@@ -0,0 +1,13 @@
+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')
+
+    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
index 270a1ebfe4..5979ceeab0 100644
--- a/var/spack/packages/py-matplotlib/package.py
+++ b/var/spack/packages/py-matplotlib/package.py
@@ -16,6 +16,7 @@ class PyMatplotlib(Package):
     depends_on('py-dateutil')
     depends_on('py-pytz')
     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-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-pyqt4/package.py b/var/spack/packages/py-pyqt4/package.py
new file mode 100644
index 0000000000..eeb1382560
--- /dev/null
+++ b/var/spack/packages/py-pyqt4/package.py
@@ -0,0 +1,18 @@
+from spack import *
+
+class PyPyqt4(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('qt')
+    depends_on('py-sip')
+
+    def install(self, spec, prefix):
+        version_array = str(spec['python'].version).split('.')
+        python('configure.py', '--confirm-license', '--destdir=%s/python%s.%s/site-packages' %(self.prefix.lib, version_array[0], version_array[1]))
+        make()
+        make('install')
diff --git a/var/spack/packages/py-sip/package.py b/var/spack/packages/py-sip/package.py
new file mode 100644
index 0000000000..06aea35a74
--- /dev/null
+++ b/var/spack/packages/py-sip/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+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')
+        make()
+        make('install')
diff --git a/var/spack/packages/qt/package.py b/var/spack/packages/qt/package.py
index 01f9de7f3c..6a55c89701 100644
--- a/var/spack/packages/qt/package.py
+++ b/var/spack/packages/qt/package.py
@@ -37,8 +37,9 @@ class Qt(Package):
                   '-fast',
                   '-optimized-qmake',
                   '-no-pch',
-                  '-no-phonon',
-                  '-no-phonon-backend',
+# phonon required for py-pyqt4
+#                  '-no-phonon',
+#                  '-no-phonon-backend',
                   '-no-openvg')
         make()
         make("install")
-- 
cgit v1.2.3-70-g09d2


From 70c8bf44b8d2613c54423562f81e049fbb956780 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 26 Jan 2015 14:47:33 -0800
Subject: Fix for install sanity check -- don't count hidden dir layout files.

---
 lib/spack/spack/package.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 43b1fcd9c8..0b6bc4ce6c 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -836,10 +836,7 @@ 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:
@@ -884,6 +881,15 @@ class Package(object):
         spack.hooks.post_install(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():
-- 
cgit v1.2.3-70-g09d2


From 6400ace90152a08a32684f97490369467ae1e37d Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 26 Jan 2015 15:45:19 -0800
Subject: Add "spack extensions" command to list activated extensions.

---
 lib/spack/spack/cmd/extensions.py | 75 +++++++++++++++++++++++++++++++++++++++
 lib/spack/spack/cmd/find.py       | 69 +++++++++++++++++++++--------------
 2 files changed, 117 insertions(+), 27 deletions(-)
 create mode 100644 lib/spack/spack/cmd/extensions.py

diff --git a/lib/spack/spack/cmd/extensions.py b/lib/spack/spack/cmd/extensions.py
new file mode 100644
index 0000000000..961d7e3f24
--- /dev/null
+++ b/lib/spack/spack/cmd/extensions.py
@@ -0,0 +1,75 @@
+##############################################################################
+# 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
+
+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.")
+
+    spec = spack.cmd.parse_specs(args.spec)
+    if len(spec) > 1:
+        tty.die("Can only list extensions for one package.")
+    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'
+
+    exts = spack.install_layout.get_extensions(spec)
+    if not exts:
+        tty.msg("%s has no activated extensions." % spec.short_spec)
+    else:
+        tty.msg("Showing %d activated extension%s for package:"
+                % (len(exts), 's' if len(exts) > 1 else ''),
+                spec.short_spec)
+        print
+        spack.cmd.find.display_specs(exts, mode=args.mode)
diff --git a/lib/spack/spack/cmd/find.py b/lib/spack/spack/cmd/find.py
index 1de3413d42..f6f503afe5 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 +83,44 @@ 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='$_$@$+', color=True),
-        else:
+
+        elif mode in ('short', 'long'):
             fmt = '$-_$@$+'
-            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'
+    display_specs(specs, mode=args.mode)
+
-- 
cgit v1.2.3-70-g09d2


From 6b90017efa1f3157fe4be7d0c7b199b6e51b9fa8 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 28 Jan 2015 22:05:57 -0800
Subject: Fixed dumb link_tree bug, added test for link tree.

---
 lib/spack/llnl/util/filesystem.py |   8 +-
 lib/spack/llnl/util/link_tree.py  | 197 ++++++++++++++++++++++----------------
 lib/spack/spack/test/__init__.py  |   3 +-
 lib/spack/spack/test/link_tree.py | 153 +++++++++++++++++++++++++++++
 4 files changed, 274 insertions(+), 87 deletions(-)
 create mode 100644 lib/spack/spack/test/link_tree.py

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/link_tree.py b/lib/spack/llnl/util/link_tree.py
index 2d7126be2c..887f6f4d26 100644
--- a/lib/spack/llnl/util/link_tree.py
+++ b/lib/spack/llnl/util/link_tree.py
@@ -29,108 +29,116 @@ import os
 import shutil
 from llnl.util.filesystem import mkdirp
 
+empty_file_name = '.spack-empty'
 
-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 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.
 
     """
-    def __init__(self, source_root):
-        self._root = source_root
+    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'.")
 
-    def traverse(self, dest_root, **kwargs):
-        """Traverse LinkTree root and dest simultaneously.
+    # List of relative paths to ignore under the src root.
+    ignore = kwargs.get('ignore', lambda filename: False)
 
-        Walks the LinkTree directory in pre or post order.  Yields
-        each file in the source directory with a matching path from
-        the dest directory.  e.g., for this tree::
+    # Don't descend into ignored directories
+    if ignore(rel_path):
+        return
 
-            root/
-              a/
-                file1
-                file2
-              b/
-                file3
+    source_path = os.path.join(source_root, rel_path)
+    dest_path   = os.path.join(dest_root, rel_path)
 
-        When called on dest, this yields::
+    # preorder yields directories before children
+    if order == 'pre':
+        yield (source_path, dest_path)
 
-            ('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')
+    for f in os.listdir(source_path):
+        source_child = os.path.join(source_path, f)
+        dest_child   = os.path.join(dest_path, f)
 
-        Optional args:
+        # Treat as a directory
+        if os.path.isdir(source_child) and (
+            follow_links or not os.path.islink(source_child)):
 
-        order=[pre|post] -- Whether to do pre- or post-order traveral.
+            # 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_child, dest_child, rel_path, **kwargs)
+                for t in tuples: yield t
 
-        ignore=<predicate> -- Predicate indicating which files to ignore.
+        # 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)
 
-        follow_nonexisting -- Whether to descend into directories in
-                              src that do not exit in dest.
 
-        """
-        # Yield directories before or after their contents.
-        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)
-
-        # Whether to descend when dirs dont' exist in dest.
-        follow_nonexisting = kwargs.get('follow_nonexisting', True)
-
-        for dirpath, dirnames, filenames in os.walk(self._root):
-            rel_path  = dirpath[len(self._root):]
-            rel_path = rel_path.lstrip(os.path.sep)
-            dest_dirpath = os.path.join(dest_root, rel_path)
-
-            # Don't descend into ignored directories
-            if ignore(dest_dirpath):
-                return
-
-            # Don't descend into dirs in dest that do not exist in src.
-            if not follow_nonexisting:
-                dirnames[:] = [
-                    d for d in dirnames
-                    if os.path.exists(os.path.join(dest_dirpath, d))]
-
-            # preorder yields directories before children
-            if order == 'pre':
-                yield (dirpath, dest_dirpath)
-
-            for name in filenames:
-                src_file  = os.path.join(dirpath, name)
-                dest_file = os.path.join(dest_dirpath, name)
-
-                # Ignore particular paths inside the install root.
-                src_relpath = src_file[len(self._root):]
-                src_relpath = src_relpath.lstrip(os.path.sep)
-                if ignore(src_relpath):
-                    continue
 
-                yield (src_file, dest_file)
+class LinkTree(object):
+    """Class to create trees of symbolic links from a source directory.
 
-            # postorder yields directories after children
-            if order == 'post':
-                yield (dirpath, dest_dirpath)
+    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 also exists in src."""
+        """Returns the first file in dest that conflicts with src"""
         kwargs['follow_nonexisting'] = False
-        for src, dest in self.traverse(dest_root, **kwargs):
-            if os.path.exists(dest) and not os.path.isdir(dest):
+        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
 
@@ -138,9 +146,20 @@ class LinkTree(object):
     def merge(self, dest_root, **kwargs):
         """Link all files in src into dest, creating directories if necessary."""
         kwargs['order'] = 'pre'
-        for src, dest in self.traverse(dest_root, **kwargs):
+        for src, dest in traverse_tree(self._root, dest_root, **kwargs):
             if os.path.isdir(src):
-                mkdirp(dest)
+                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)
@@ -153,12 +172,20 @@ class LinkTree(object):
 
         """
         kwargs['order'] = 'post'
-        for src, dest in self.traverse(dest_root, **kwargs):
-            if os.path.isdir(dest):
+        for src, dest in traverse_tree(self._root, dest_root, **kwargs):
+            if os.path.isdir(src):
+                if not os.path.isdir(dest):
+                    raise ValueError("File blocks directory: %s" % dest)
+
+                # remove directory if it is empty.
                 if not os.listdir(dest):
-                    # TODO: what if empty directories were present pre-merge?
                     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)
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'))
-- 
cgit v1.2.3-70-g09d2


From 2d9190d264dd276853aca41998fffbab1baecdb0 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 2 Feb 2015 06:09:35 -0800
Subject: Add extensions command.

---
 lib/spack/llnl/util/link_tree.py         |  5 ++-
 lib/spack/spack/cmd/extensions.py        |  9 ++--
 lib/spack/spack/directory_layout.py      |  2 +-
 lib/spack/spack/package.py               |  5 +++
 lib/spack/spack/packages.py              |  5 +++
 lib/spack/spack/spec.py                  |  7 +++
 var/spack/packages/py-basemap/package.py |  1 +
 var/spack/packages/python/package.py     | 77 +++++++++++++++++++++++++++++---
 8 files changed, 99 insertions(+), 12 deletions(-)

diff --git a/lib/spack/llnl/util/link_tree.py b/lib/spack/llnl/util/link_tree.py
index 887f6f4d26..4e4e48316e 100644
--- a/lib/spack/llnl/util/link_tree.py
+++ b/lib/spack/llnl/util/link_tree.py
@@ -27,7 +27,7 @@ __all__ = ['LinkTree']
 
 import os
 import shutil
-from llnl.util.filesystem import mkdirp
+from llnl.util.filesystem import *
 
 empty_file_name = '.spack-empty'
 
@@ -93,6 +93,7 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
     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 (
@@ -101,7 +102,7 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
             # 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_child, dest_child, rel_path, **kwargs)
+                tuples = traverse_tree(source_root, dest_root, rel_child, **kwargs)
                 for t in tuples: yield t
 
         # Treat as a file.
diff --git a/lib/spack/spack/cmd/extensions.py b/lib/spack/spack/cmd/extensions.py
index 961d7e3f24..f28a388bf2 100644
--- a/lib/spack/spack/cmd/extensions.py
+++ b/lib/spack/spack/cmd/extensions.py
@@ -26,6 +26,7 @@ import sys
 from external import argparse
 
 import llnl.util.tty as tty
+from llnl.util.tty.colify import colify
 
 import spack
 import spack.cmd
@@ -66,10 +67,10 @@ def extensions(parser, args):
 
     exts = spack.install_layout.get_extensions(spec)
     if not exts:
-        tty.msg("%s has no activated extensions." % spec.short_spec)
+        tty.msg("%s has no activated extensions." % spec.cshort_spec)
     else:
-        tty.msg("Showing %d activated extension%s for package:"
-                % (len(exts), 's' if len(exts) > 1 else ''),
-                spec.short_spec)
+        tty.msg("Extensions for package %s:" % spec.cshort_spec)
+        colify(pkg.name for pkg in spack.db.extensions_for(spec))
         print
+        tty.msg("%d currently activated:" % len(exts))
         spack.cmd.find.display_specs(exts, mode=args.mode)
diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index ff327ed504..efc40a17a4 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -269,8 +269,8 @@ class SpecHashDirectoryLayout(DirectoryLayout):
     def get_extensions(self, spec):
         _check_concrete(spec)
 
-        path = self.extension_file_path(spec)
         extensions = set()
+        path = self.extension_file_path(spec)
         if os.path.exists(path):
             with closing(open(path)) as ext_file:
                 for line in ext_file:
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 0b6bc4ce6c..b905968540 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -522,6 +522,11 @@ class Package(object):
         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.spec.concrete:
diff --git a/lib/spack/spack/packages.py b/lib/spack/spack/packages.py
index bb5a94bcab..b3049e812f 100644
--- a/lib/spack/spack/packages.py
+++ b/lib/spack/spack/packages.py
@@ -112,6 +112,11 @@ 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)]
+
+
     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."""
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
@@ -552,6 +552,13 @@ class Spec(object):
         return self.format('$_$@$%@$+$=$#')
 
 
+    @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/var/spack/packages/py-basemap/package.py b/var/spack/packages/py-basemap/package.py
index 8955bf8827..7b6d8e7e65 100644
--- a/var/spack/packages/py-basemap/package.py
+++ b/var/spack/packages/py-basemap/package.py
@@ -11,6 +11,7 @@ class PyBasemap(Package):
     geos_version = {'1.0.7' : '3.3.3'}
 
     extends('python')
+    depends_on('py-setuptools')
     depends_on('py-numpy')
     depends_on('py-matplotlib')
     depends_on('py-pil')
diff --git a/var/spack/packages/python/package.py b/var/spack/packages/python/package.py
index a22bd54c82..8a6d574d9b 100644
--- a/var/spack/packages/python/package.py
+++ b/var/spack/packages/python/package.py
@@ -1,6 +1,9 @@
 from spack import *
+import spack
 import os
 import re
+from contextlib import closing
+
 
 class Python(Package):
     """The Python programming language."""
@@ -29,6 +32,10 @@ class Python(Package):
         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])
@@ -60,21 +67,81 @@ class Python(Package):
         mkdirp(module.site_packages_dir)
 
 
-    def make_ignore(self, args):
+    # ========================================================================
+    # Handle specifics of activating and deactivating python modules.
+    # ========================================================================
+
+    def python_ignore(self, ext_pkg, args):
         """Add some ignore files to activate/deactivate args."""
         orig_ignore = args.get('ignore', lambda f: False)
+
         def ignore(filename):
-            return (re.search(r'/site\.pyc?$', filename) or
-                    re.search(r'\.pth$', filename) or
+            # 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 (any(re.search(p, filename) for p in patterns) or
                     orig_ignore(filename))
+
         return ignore
 
 
+    def write_easy_install_pth(self, extensions):
+        paths = []
+        for ext in extensions:
+            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.make_ignore(args))
+        args.update(ignore=self.python_ignore(ext_pkg, args))
         super(Python, self).activate(ext_pkg, **args)
 
+        extensions = set(spack.install_layout.get_extensions(self.spec))
+        extensions.add(ext_pkg.spec)
+        self.write_easy_install_pth(extensions)
+
 
     def deactivate(self, ext_pkg, **args):
-        args.update(ignore=self.make_ignore(args))
+        args.update(ignore=self.python_ignore(ext_pkg, args))
         super(Python, self).deactivate(ext_pkg, **args)
+
+        extensions = set(spack.install_layout.get_extensions(self.spec))
+        extensions.remove(ext_pkg.spec)
+        self.write_easy_install_pth(extensions)
-- 
cgit v1.2.3-70-g09d2


From 5bde8359e8378bf8595a4bef343d1f50258f663d Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 2 Feb 2015 07:58:52 -0800
Subject: More information in extensions command.

---
 lib/spack/spack/cmd/extensions.py | 39 ++++++++++++++++++++++++++++++---------
 lib/spack/spack/packages.py       |  6 ++++++
 2 files changed, 36 insertions(+), 9 deletions(-)

diff --git a/lib/spack/spack/cmd/extensions.py b/lib/spack/spack/cmd/extensions.py
index f28a388bf2..f6ccd7b515 100644
--- a/lib/spack/spack/cmd/extensions.py
+++ b/lib/spack/spack/cmd/extensions.py
@@ -54,9 +54,14 @@ 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:
@@ -65,12 +70,28 @@ def extensions(parser, args):
     if not args.mode:
         args.mode = 'short'
 
-    exts = spack.install_layout.get_extensions(spec)
-    if not exts:
-        tty.msg("%s has no activated extensions." % spec.cshort_spec)
-    else:
-        tty.msg("Extensions for package %s:" % spec.cshort_spec)
-        colify(pkg.name for pkg in spack.db.extensions_for(spec))
-        print
-        tty.msg("%d currently activated:" % len(exts))
-        spack.cmd.find.display_specs(exts, mode=args.mode)
+    # 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("%s extensions:" % spec.cshort_spec)
+    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 activated.")
+        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.get_extensions(spec)
+    print
+    if not activated:
+        tty.msg("None activated.")
+        return
+    tty.msg("%d currently activated:" % len(exts))
+    spack.cmd.find.display_specs(installed, mode=args.mode)
diff --git a/lib/spack/spack/packages.py b/lib/spack/spack/packages.py
index b3049e812f..7ef8135c1a 100644
--- a/lib/spack/spack/packages.py
+++ b/lib/spack/spack/packages.py
@@ -117,6 +117,12 @@ class PackageDB(object):
         return [p for p in self.all_packages() if p.extends(extendee_spec)]
 
 
+    @_autospec
+    def installed_extensions_for(self, extendee_spec):
+        return [s.package for s in self.installed_package_specs()
+                if s.package.extends(extendee_spec)]
+
+
     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."""
-- 
cgit v1.2.3-70-g09d2


From a9e189972a547fb5f7996f0f5acafc1200702b72 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 4 Feb 2015 15:42:41 -0800
Subject: Bugfix in spak extensions

---
 lib/spack/spack/cmd/extensions.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/cmd/extensions.py b/lib/spack/spack/cmd/extensions.py
index f6ccd7b515..3b189895b0 100644
--- a/lib/spack/spack/cmd/extensions.py
+++ b/lib/spack/spack/cmd/extensions.py
@@ -93,5 +93,5 @@ def extensions(parser, args):
     if not activated:
         tty.msg("None activated.")
         return
-    tty.msg("%d currently activated:" % len(exts))
-    spack.cmd.find.display_specs(installed, mode=args.mode)
+    tty.msg("%d currently activated:" % len(activated))
+    spack.cmd.find.display_specs(activated, mode=args.mode)
-- 
cgit v1.2.3-70-g09d2


From 3a3e4d4391977327bca18c416205971dd6a85509 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 4 Feb 2015 15:47:03 -0800
Subject: Do not automatically activate extensions on install.

---
 lib/spack/spack/hooks/extensions.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/lib/spack/spack/hooks/extensions.py b/lib/spack/spack/hooks/extensions.py
index 718b24b965..9d6fa23d03 100644
--- a/lib/spack/spack/hooks/extensions.py
+++ b/lib/spack/spack/hooks/extensions.py
@@ -26,15 +26,11 @@
 import spack
 
 
-def post_install(pkg):
-    if pkg.is_extension:
-        pkg.do_activate()
-
-
 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:
-        pkg.do_deactivate()
+        if pkg.activated:
+            pkg.do_deactivate()
-- 
cgit v1.2.3-70-g09d2


From 5cc369c2b831446f1afaaba41cbf0dbdba75b4ed Mon Sep 17 00:00:00 2001
From: "Gregory L. Lee" <lee218@llnl.gov>
Date: Fri, 6 Feb 2015 16:35:35 -0800
Subject: add dependent packages to PYTHONPATH for build

---
 var/spack/packages/python/package.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/var/spack/packages/python/package.py b/var/spack/packages/python/package.py
index 8a6d574d9b..23b528b089 100644
--- a/var/spack/packages/python/package.py
+++ b/var/spack/packages/python/package.py
@@ -66,6 +66,11 @@ class Python(Package):
         # Make the site packages directory if it does not exist already.
         mkdirp(module.site_packages_dir)
 
+        # Add dependent packages' site-packages directory to PYTHONPATH
+        for d in ext_spec.traverse():
+            if d.package.extends(self.spec):
+                os.environ['PYTHONPATH'] += ':' + os.path.join(d.prefix, self.site_packages_dir)
+
 
     # ========================================================================
     # Handle specifics of activating and deactivating python modules.
-- 
cgit v1.2.3-70-g09d2


From befe72b9b9d1f4107eef8f24e6f194f27a15bca4 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 8 Feb 2015 19:36:30 -0800
Subject: directory_layout now raises an error when an install fails.

---
 lib/spack/spack/directory_layout.py | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index efc40a17a4..37740720a2 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -109,12 +109,17 @@ 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:
@@ -330,6 +335,15 @@ 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):
@@ -370,3 +384,5 @@ class NoSuchExtensionError(DirectoryLayoutError):
         super(NoSuchExtensionError, self).__init__(
             "%s cannot be removed from %s because it's not installed."% (
                 extension_spec.short_spec, spec.short_spec))
+
+
-- 
cgit v1.2.3-70-g09d2


From e51e01f4f066f9b0f412354cb8abab3642845d43 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 8 Feb 2015 19:39:36 -0800
Subject: Cleaned up python to remove redundant line.

---
 var/spack/packages/python/package.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/var/spack/packages/python/package.py b/var/spack/packages/python/package.py
index 23b528b089..8bffbf393c 100644
--- a/var/spack/packages/python/package.py
+++ b/var/spack/packages/python/package.py
@@ -60,16 +60,16 @@ class Python(Package):
         module.python_lib_dir = os.path.join(ext_spec.prefix, self.python_lib_dir)
         module.site_packages_dir = os.path.join(ext_spec.prefix, self.site_packages_dir)
 
-        # Add site packages directory to the PYTHONPATH
-        os.environ['PYTHONPATH'] = module.site_packages_dir
-
         # Make the site packages directory if it does not exist already.
         mkdirp(module.site_packages_dir)
 
-        # Add dependent packages' site-packages directory to PYTHONPATH
+        # 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):
-                os.environ['PYTHONPATH'] += ':' + os.path.join(d.prefix, self.site_packages_dir)
+                python_paths.append(os.path.join(d.prefix, self.site_packages_dir))
+        os.environ['PYTHONPATH'] = ':'.join(python_paths)
 
 
     # ========================================================================
-- 
cgit v1.2.3-70-g09d2


From 60a385d4a44b16bce77725dbb4f71a26aa610ffc Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 8 Feb 2015 19:40:28 -0800
Subject: Minor textual error in extensions command.

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

diff --git a/lib/spack/spack/cmd/extensions.py b/lib/spack/spack/cmd/extensions.py
index 3b189895b0..c6b6145321 100644
--- a/lib/spack/spack/cmd/extensions.py
+++ b/lib/spack/spack/cmd/extensions.py
@@ -82,7 +82,7 @@ def extensions(parser, args):
     installed  = [s.spec for s in spack.db.installed_extensions_for(spec)]
     print
     if not installed:
-        tty.msg("None activated.")
+        tty.msg("None installed.")
         return
     tty.msg("%d installed:" % len(installed))
     spack.cmd.find.display_specs(installed, mode=args.mode)
-- 
cgit v1.2.3-70-g09d2


From 20ec80295dbf2a36b633860c139d113f9c0e6388 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 8 Feb 2015 19:41:17 -0800
Subject: setup_extension_environment is now setup_dependent_environment.

- other packages, like Qt, can now use this to set up relevant build
  variables and env vars for their dependencies.

- not just extensions anymore.
---
 lib/spack/spack/package.py           | 14 ++++++++------
 var/spack/packages/python/package.py |  2 +-
 var/spack/packages/qt/package.py     |  6 ++++++
 3 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index b905968540..6e319a1f87 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -829,10 +829,10 @@ class Package(object):
                 self.stage.chdir_to_source()
                 build_env.setup_package(self)
 
-                # Allow extendees to further set up the environment.
-                if self.is_extension:
-                    self.extendee_spec.package.setup_extension_environment(
-                        self.module, self.extendee_spec, self.spec)
+                # Allow dependencies to further set up the environment.
+                for dep_spec in self.spec.traverse(root=False):
+                    dep_spec.package.setup_dependent_environment(
+                        self.module, dep_spec, self.spec)
 
                 if fake_install:
                     self.do_fake_install()
@@ -910,8 +910,8 @@ class Package(object):
                           fromlist=[self.__class__.__name__])
 
 
-    def setup_extension_environment(self, module, spec, ext_spec):
-        """Called before the install() method of extensions.
+    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
@@ -930,6 +930,8 @@ class Package(object):
            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
 
diff --git a/var/spack/packages/python/package.py b/var/spack/packages/python/package.py
index 8bffbf393c..eed81d095c 100644
--- a/var/spack/packages/python/package.py
+++ b/var/spack/packages/python/package.py
@@ -46,7 +46,7 @@ class Python(Package):
         return os.path.join(self.python_lib_dir, 'site-packages')
 
 
-    def setup_extension_environment(self, module, spec, ext_spec):
+    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::
diff --git a/var/spack/packages/qt/package.py b/var/spack/packages/qt/package.py
index 6a55c89701..fcbcd2491a 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'
-- 
cgit v1.2.3-70-g09d2


From f81b136547347997d043bd99adf9d7013f097c69 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 8 Feb 2015 19:43:10 -0800
Subject: import fix in cmd/clean

---
 lib/spack/spack/cmd/clean.py | 1 +
 1 file changed, 1 insertion(+)

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
 
-- 
cgit v1.2.3-70-g09d2


From c077f0570531aac76b9182a96a2a37ee0e633989 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 8 Feb 2015 22:01:00 -0800
Subject: Move dpeendency environment setup to build_environemnt.

---
 lib/spack/spack/build_environment.py | 5 +++++
 lib/spack/spack/package.py           | 5 -----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 45353ec640..cabde7dc86 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -207,3 +207,8 @@ 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)
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 6e319a1f87..b18d054990 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -829,11 +829,6 @@ class Package(object):
                 self.stage.chdir_to_source()
                 build_env.setup_package(self)
 
-                # Allow dependencies to further set up the environment.
-                for dep_spec in self.spec.traverse(root=False):
-                    dep_spec.package.setup_dependent_environment(
-                        self.module, dep_spec, self.spec)
-
                 if fake_install:
                     self.do_fake_install()
                 else:
-- 
cgit v1.2.3-70-g09d2


From aae364b4c9ffdf8949a8c7ce5a7e63c9772703c0 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 8 Feb 2015 23:26:15 -0800
Subject: "spack extensions" shows total extension count.

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

diff --git a/lib/spack/spack/cmd/extensions.py b/lib/spack/spack/cmd/extensions.py
index c6b6145321..ae73d8ac55 100644
--- a/lib/spack/spack/cmd/extensions.py
+++ b/lib/spack/spack/cmd/extensions.py
@@ -75,7 +75,8 @@ def extensions(parser, args):
     if not extensions:
         tty.msg("%s has no extensions." % spec.cshort_spec)
         return
-    tty.msg("%s extensions:" % spec.cshort_spec)
+    tty.msg(spec.cshort_spec)
+    tty.msg("%d extensions:" % len(extensions))
     colify(ext.name for ext in extensions)
 
     # List specs of installed extensions.
-- 
cgit v1.2.3-70-g09d2


From 25af341954fa7c9a88943fe24cad88275ee00795 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 9 Feb 2015 02:54:49 -0800
Subject: Python package improvements.

---
 var/spack/packages/geos/package.py          | 31 +++++++++++++++++++++++++++++
 var/spack/packages/py-basemap/package.py    |  9 ++-------
 var/spack/packages/py-biopython/package.py  |  1 +
 var/spack/packages/py-gnuplot/package.py    |  1 +
 var/spack/packages/py-libxml2/package.py    |  1 +
 var/spack/packages/py-matplotlib/package.py |  3 +++
 var/spack/packages/py-pyside/package.py     | 31 +++++++++++++++++++++++++----
 var/spack/packages/py-shiboken/package.py   | 21 +++++++++++++++++++
 var/spack/packages/python/package.py        |  5 +++--
 9 files changed, 90 insertions(+), 13 deletions(-)
 create mode 100644 var/spack/packages/geos/package.py
 create mode 100644 var/spack/packages/py-shiboken/package.py

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/py-basemap/package.py b/var/spack/packages/py-basemap/package.py
index 7b6d8e7e65..45f1085ba1 100644
--- a/var/spack/packages/py-basemap/package.py
+++ b/var/spack/packages/py-basemap/package.py
@@ -8,18 +8,13 @@ class PyBasemap(Package):
 
     version('1.0.7', '48c0557ced9e2c6e440b28b3caff2de8')
 
-    geos_version = {'1.0.7' : '3.3.3'}
-
     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):
-        with working_dir('geos-%s' % self.geos_version[str(self.version)]):
-            configure("--prefix=" + prefix)
-            make()
-            make("install")
-        os.environ['GEOS_DIR'] = 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
index 2ed04c389e..8ecaf48626 100644
--- a/var/spack/packages/py-biopython/package.py
+++ b/var/spack/packages/py-biopython/package.py
@@ -9,6 +9,7 @@ class PyBiopython(Package):
 
     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-gnuplot/package.py b/var/spack/packages/py-gnuplot/package.py
index 0a2c073a49..ede4472c03 100644
--- a/var/spack/packages/py-gnuplot/package.py
+++ b/var/spack/packages/py-gnuplot/package.py
@@ -8,6 +8,7 @@ class PyGnuplot(Package):
     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-libxml2/package.py b/var/spack/packages/py-libxml2/package.py
index 0dcefbd9cf..e645acb5dd 100644
--- a/var/spack/packages/py-libxml2/package.py
+++ b/var/spack/packages/py-libxml2/package.py
@@ -8,6 +8,7 @@ class PyLibxml2(Package):
     version('2.6.21', '229dd2b3d110a77defeeaa73af83f7f3')
 
     extends('python')
+    depends_on('libxml2')
 
     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
index 5979ceeab0..8b8684c563 100644
--- a/var/spack/packages/py-matplotlib/package.py
+++ b/var/spack/packages/py-matplotlib/package.py
@@ -17,9 +17,12 @@ class PyMatplotlib(Package):
     depends_on('py-pytz')
     depends_on('py-nose')
     depends_on('py-numpy')
+    depends_on('qt')
+
 
     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
diff --git a/var/spack/packages/py-pyside/package.py b/var/spack/packages/py-pyside/package.py
index b01e16d7e6..7528a0bf72 100644
--- a/var/spack/packages/py-pyside/package.py
+++ b/var/spack/packages/py-pyside/package.py
@@ -10,9 +10,32 @@ class PyPyside(Package):
     version('1.2.2', 'c45bc400c8a86d6b35f34c29e379e44d')
 
     extends('python')
+    depends_on('py-setuptools')
+    depends_on('qt@:4')
+
+
+    def patch(Self):
+        """Undo PySide 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.
+        filter_file(
+            r'OPTION_CMAKE,',
+            r'OPTION_CMAKE, ' + (
+                '"-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE", '
+                '"-DCMAKE_INSTALL_RPATH=%s",' % ':'.join(self.rpath)),
+            'setup.py')
+
+        # PySide tries to patch ELF files to remove RPATHs
+        # Disable this and go with the one we set.
+        filter_file(
+            r'rpath_cmd\(pyside_path, srcpath\)',
+            r'#rpath_cmd(pyside_path, srcpath)',
+            'pyside_postinstall.py')
+
 
     def install(self, spec, prefix):
-        qmake_path = '/usr/lib64/qt4/bin/qmake'
-        if not os.path.exists(qmake_path):
-            raise spack.package.InstallError("Failed to find qmake in %s" % qmake_path)
-        python('setup.py', 'install', '--prefix=%s' % prefix, '--qmake=%s' % qmake_path)
+        python('setup.py', 'install',
+               '--prefix=%s' % prefix,
+               '--jobs=%s' % make_jobs)
+
+
diff --git a/var/spack/packages/py-shiboken/package.py b/var/spack/packages/py-shiboken/package.py
new file mode 100644
index 0000000000..47abe64e65
--- /dev/null
+++ b/var/spack/packages/py-shiboken/package.py
@@ -0,0 +1,21 @@
+from spack import *
+
+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 install(self, spec, prefix):
+        python('setup.py', 'install',
+               '--prefix=%s' % prefix,
+               '--jobs=%s' % make_jobs)
diff --git a/var/spack/packages/python/package.py b/var/spack/packages/python/package.py
index eed81d095c..4b3b31eb6b 100644
--- a/var/spack/packages/python/package.py
+++ b/var/spack/packages/python/package.py
@@ -1,9 +1,10 @@
-from spack import *
-import spack
 import os
 import re
 from contextlib import closing
 
+from spack import *
+import spack
+
 
 class Python(Package):
     """The Python programming language."""
-- 
cgit v1.2.3-70-g09d2


From 5c2608b032f04c063c437eca7d8360baaf6a2a16 Mon Sep 17 00:00:00 2001
From: "Gregory L. Lee" <lee218@llnl.gov>
Date: Mon, 9 Feb 2015 15:55:18 -0800
Subject: typo: Self -> self

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

diff --git a/var/spack/packages/py-pyside/package.py b/var/spack/packages/py-pyside/package.py
index 7528a0bf72..1fd037d75f 100644
--- a/var/spack/packages/py-pyside/package.py
+++ b/var/spack/packages/py-pyside/package.py
@@ -14,7 +14,7 @@ class PyPyside(Package):
     depends_on('qt@:4')
 
 
-    def patch(Self):
+    def patch(self):
         """Undo PySide 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.
-- 
cgit v1.2.3-70-g09d2


From 82dc935a50874e899380f32a9a35b7cc4f76df87 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 15 Feb 2015 01:49:50 -0800
Subject: installed_extensions_for no longer fails when nothing known about pkg

---
 lib/spack/spack/packages.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/packages.py b/lib/spack/spack/packages.py
index 7ef8135c1a..3c81863c11 100644
--- a/lib/spack/spack/packages.py
+++ b/lib/spack/spack/packages.py
@@ -119,8 +119,15 @@ class PackageDB(object):
 
     @_autospec
     def installed_extensions_for(self, extendee_spec):
-        return [s.package for s in self.installed_package_specs()
-                if s.package.extends(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):
-- 
cgit v1.2.3-70-g09d2


From c0c08799249fb56c281f62b3659e7cf7d7080188 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 15 Feb 2015 01:58:35 -0800
Subject: Better extension activation/deactivation

---
 lib/spack/spack/cmd/extensions.py    |   4 +-
 lib/spack/spack/directory_layout.py  | 150 +++++++++++++++++++++++++----------
 lib/spack/spack/package.py           |  19 ++++-
 var/spack/packages/python/package.py |  16 ++--
 4 files changed, 133 insertions(+), 56 deletions(-)

diff --git a/lib/spack/spack/cmd/extensions.py b/lib/spack/spack/cmd/extensions.py
index ae73d8ac55..fc8e6842c3 100644
--- a/lib/spack/spack/cmd/extensions.py
+++ b/lib/spack/spack/cmd/extensions.py
@@ -89,10 +89,10 @@ def extensions(parser, args):
     spack.cmd.find.display_specs(installed, mode=args.mode)
 
     # List specs of activated extensions.
-    activated  = spack.install_layout.get_extensions(spec)
+    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, mode=args.mode)
+    spack.cmd.find.display_specs(activated.values(), mode=args.mode)
diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index 37740720a2..562c0bd3ed 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -27,6 +27,7 @@ import os
 import exceptions
 import hashlib
 import shutil
+import tempfile
 from contextlib import closing
 
 import llnl.util.tty as tty
@@ -84,17 +85,38 @@ class DirectoryLayout(object):
         raise NotImplementedError()
 
 
-    def get_extensions(self, spec):
-        """Get a set of currently installed extension packages for a spec."""
+    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, extension_spec):
+    def add_extension(self, spec, ext_spec):
         """Add to the list of currently installed extensions."""
         raise NotImplementedError()
 
 
-    def remove_extension(self, spec, extension_spec):
+    def remove_extension(self, spec, ext_spec):
         """Remove from the list of currently installed extensions."""
         raise NotImplementedError()
 
@@ -173,6 +195,8 @@ class SpecHashDirectoryLayout(DirectoryLayout):
         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):
@@ -271,54 +295,94 @@ class SpecHashDirectoryLayout(DirectoryLayout):
         return join_path(self.path_for_spec(spec), self.extension_file_name)
 
 
-    def get_extensions(self, spec):
+    def _extension_map(self, spec):
+        """Get a dict<name -> spec> for all extensions currnetly
+           installed for this package."""
         _check_concrete(spec)
 
-        extensions = set()
-        path = self.extension_file_path(spec)
-        if os.path.exists(path):
-            with closing(open(path)) as ext_file:
-                for line in ext_file:
-                    try:
-                        extensions.add(Spec(line.strip()))
-                    except spack.error.SpackError, e:
-                        raise InvalidExtensionSpecError(str(e))
-        return extensions
+        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):
+
+    def _write_extensions(self, spec, extensions):
         path = self.extension_file_path(spec)
-        with closing(open(path, 'w')) as spec_file:
-            for extension in sorted(extensions):
-                spec_file.write("%s\n" % extension)
+
+        # 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, extension_spec):
+    def add_extension(self, spec, ext_spec):
         _check_concrete(spec)
-        _check_concrete(extension_spec)
+        _check_concrete(ext_spec)
 
-        exts = self.get_extensions(spec)
-        if extension_spec in exts:
-            raise ExtensionAlreadyInstalledError(spec, extension_spec)
-        else:
-            for already_installed in exts:
-                if spec.name == extension_spec.name:
-                    raise ExtensionConflictError(spec, extension_spec, already_installed)
+        # Check whether it's already installed or if it's a conflict.
+        exts = self.extension_map(spec)
+        self.check_extension_conflict(spec, ext_spec)
 
-        exts.add(extension_spec)
-        self.write_extensions(spec, exts)
+        # do the actual adding.
+        exts[ext_spec.name] = ext_spec
+        self._write_extensions(spec, exts)
 
 
-    def remove_extension(self, spec, extension_spec):
+    def remove_extension(self, spec, ext_spec):
         _check_concrete(spec)
-        _check_concrete(extension_spec)
+        _check_concrete(ext_spec)
 
-        exts = self.get_extensions(spec)
-        if not extension_spec in exts:
-            raise NoSuchExtensionError(spec, extension_spec)
+        # Make sure it's installed before removing.
+        exts = self.extension_map(spec)
+        self.check_activated(spec, ext_spec)
 
-        exts.remove(extension_spec)
-        self.write_extensions(spec, exts)
+        # do the actual removing.
+        del exts[ext_spec.name]
+        self._write_extensions(spec, exts)
 
 
 class DirectoryLayoutError(SpackError):
@@ -365,24 +429,24 @@ class InvalidExtensionSpecError(DirectoryLayoutError):
 
 class ExtensionAlreadyInstalledError(DirectoryLayoutError):
     """Raised when an extension is added to a package that already has it."""
-    def __init__(self, spec, extension_spec):
+    def __init__(self, spec, ext_spec):
         super(ExtensionAlreadyInstalledError, self).__init__(
-            "%s is already installed in %s" % (extension_spec.short_spec, spec.short_spec))
+            "%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, extension_spec, conflict):
+    def __init__(self, spec, ext_spec, conflict):
         super(ExtensionConflictError, self).__init__(
             "%s cannot be installed in %s because it conflicts with %s."% (
-                extension_spec.short_spec, spec.short_spec, conflict.short_spec))
+                ext_spec.short_spec, spec.short_spec, conflict.short_spec))
 
 
 class NoSuchExtensionError(DirectoryLayoutError):
     """Raised when an extension isn't there on remove."""
-    def __init__(self, spec, extension_spec):
+    def __init__(self, spec, ext_spec):
         super(NoSuchExtensionError, self).__init__(
             "%s cannot be removed from %s because it's not installed."% (
-                extension_spec.short_spec, spec.short_spec))
+                ext_spec.short_spec, spec.short_spec))
 
 
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index b18d054990..a624c1ebf5 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -534,7 +534,8 @@ class Package(object):
         if not self.is_extension:
             raise ValueError("is_extension called on package that is not an extension.")
 
-        return self.spec in spack.install_layout.get_extensions(self.extendee_spec)
+        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):
@@ -987,6 +988,8 @@ class Package(object):
         activate() directly.
         """
         self._sanity_check_extension()
+        spack.install_layout.check_extension_conflict(self.extendee_spec, self.spec)
+
         self.extendee_spec.package.activate(self, **self.extendee_args)
 
         spack.install_layout.add_extension(self.extendee_spec, self.spec)
@@ -1014,12 +1017,22 @@ class Package(object):
         tree.merge(self.prefix, ignore=ignore)
 
 
-    def do_deactivate(self):
+    def do_deactivate(self, **kwargs):
         """Called on the extension to invoke extendee's deactivate() method."""
+        force = kwargs.get('force', False)
+
         self._sanity_check_extension()
+
+        # 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)
+
         self.extendee_spec.package.deactivate(self, **self.extendee_args)
 
-        if self.spec in spack.install_layout.get_extensions(self.extendee_spec):
+        # 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."
diff --git a/var/spack/packages/python/package.py b/var/spack/packages/python/package.py
index 4b3b31eb6b..de7f412b52 100644
--- a/var/spack/packages/python/package.py
+++ b/var/spack/packages/python/package.py
@@ -98,9 +98,9 @@ class Python(Package):
         return ignore
 
 
-    def write_easy_install_pth(self, extensions):
+    def write_easy_install_pth(self, exts):
         paths = []
-        for ext in extensions:
+        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
 
@@ -139,15 +139,15 @@ class Python(Package):
         args.update(ignore=self.python_ignore(ext_pkg, args))
         super(Python, self).activate(ext_pkg, **args)
 
-        extensions = set(spack.install_layout.get_extensions(self.spec))
-        extensions.add(ext_pkg.spec)
-        self.write_easy_install_pth(extensions)
+        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)
 
-        extensions = set(spack.install_layout.get_extensions(self.spec))
-        extensions.remove(ext_pkg.spec)
-        self.write_easy_install_pth(extensions)
+        exts = spack.install_layout.extension_map(self.spec)
+        del exts[ext_pkg.name]
+        self.write_easy_install_pth(exts)
-- 
cgit v1.2.3-70-g09d2


From 3c0048dd89e4d18ac95afd19b65d7ce54a48d862 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 15 Feb 2015 01:59:36 -0800
Subject: py-sip installs properly into a prefix

---
 var/spack/packages/py-sip/package.py |  7 ++++++-
 var/spack/packages/python/package.py | 10 ++++++++--
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/var/spack/packages/py-sip/package.py b/var/spack/packages/py-sip/package.py
index 06aea35a74..6753bdd2a5 100644
--- a/var/spack/packages/py-sip/package.py
+++ b/var/spack/packages/py-sip/package.py
@@ -1,4 +1,5 @@
 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."""
@@ -10,6 +11,10 @@ class PySip(Package):
     extends('python')
 
     def install(self, spec, prefix):
-        python('configure.py')
+        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/python/package.py b/var/spack/packages/python/package.py
index de7f412b52..fb875a7eeb 100644
--- a/var/spack/packages/python/package.py
+++ b/var/spack/packages/python/package.py
@@ -42,6 +42,11 @@ class Python(Package):
         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')
@@ -58,8 +63,9 @@ class Python(Package):
         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.site_packages_dir = os.path.join(ext_spec.prefix, self.site_packages_dir)
+        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)
-- 
cgit v1.2.3-70-g09d2


From d1e03329c5c16ba38b082c3473e7c6970f168990 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 15 Feb 2015 11:50:13 -0800
Subject: Memoize all_specs() and exists() for better performance.

- Real bottleneck is calling normalize() for every spec when we read it.
- Need to store graph information in spec files to avoid the need for this.
  - Also, normalizing old specs isn't always possible, so we need to do this anyway.
---
 lib/spack/spack/directory_layout.py | 11 +++++++++--
 lib/spack/spack/packages.py         |  1 +
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index 562c0bd3ed..5b80e93d6b 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -31,6 +31,7 @@ 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
@@ -223,6 +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.
@@ -276,17 +280,20 @@ 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):
diff --git a/lib/spack/spack/packages.py b/lib/spack/spack/packages.py
index 3c81863c11..43c4c191c1 100644
--- a/lib/spack/spack/packages.py
+++ b/lib/spack/spack/packages.py
@@ -192,6 +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))
-- 
cgit v1.2.3-70-g09d2


From 2f67cdaf10a3e64474f7ac242518fdfe93e9c87a Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 15 Feb 2015 12:39:10 -0800
Subject: Better time output on build completion.

---
 lib/spack/spack/package.py             | 16 ++++++++++++++--
 var/spack/packages/py-pyqt/package.py  | 21 +++++++++++++++++++++
 var/spack/packages/py-pyqt4/package.py | 18 ------------------
 3 files changed, 35 insertions(+), 20 deletions(-)
 create mode 100644 var/spack/packages/py-pyqt/package.py
 delete mode 100644 var/spack/packages/py-pyqt4/package.py

diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index a624c1ebf5..c48816cb5b 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -848,8 +848,8 @@ 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,
@@ -1201,6 +1201,18 @@ 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):
diff --git a/var/spack/packages/py-pyqt/package.py b/var/spack/packages/py-pyqt/package.py
new file mode 100644
index 0000000000..cb40af351a
--- /dev/null
+++ b/var/spack/packages/py-pyqt/package.py
@@ -0,0 +1,21 @@
+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('qt@4')  # TODO: allow qt5 when conditional deps are supported.
+    depends_on('py-sip')
+
+    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-pyqt4/package.py b/var/spack/packages/py-pyqt4/package.py
deleted file mode 100644
index eeb1382560..0000000000
--- a/var/spack/packages/py-pyqt4/package.py
+++ /dev/null
@@ -1,18 +0,0 @@
-from spack import *
-
-class PyPyqt4(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('qt')
-    depends_on('py-sip')
-
-    def install(self, spec, prefix):
-        version_array = str(spec['python'].version).split('.')
-        python('configure.py', '--confirm-license', '--destdir=%s/python%s.%s/site-packages' %(self.prefix.lib, version_array[0], version_array[1]))
-        make()
-        make('install')
-- 
cgit v1.2.3-70-g09d2


From b11061f99d9e501f69d6d39bae56f0b69d17eaa1 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 15 Feb 2015 12:40:02 -0800
Subject: Rename py-pyqt4 to py-pyqt.

---
 var/spack/packages/py-pyqt/package.py | 5 ++++-
 var/spack/packages/qt/package.py      | 6 +++---
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/var/spack/packages/py-pyqt/package.py b/var/spack/packages/py-pyqt/package.py
index cb40af351a..8edca105bb 100644
--- a/var/spack/packages/py-pyqt/package.py
+++ b/var/spack/packages/py-pyqt/package.py
@@ -10,9 +10,12 @@ class PyPyqt(Package):
     version('4.11.3', '997c3e443165a89a559e0d96b061bf70')
 
     extends('python')
-    depends_on('qt@4')  # TODO: allow qt5 when conditional deps are supported.
     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',
diff --git a/var/spack/packages/qt/package.py b/var/spack/packages/qt/package.py
index fcbcd2491a..3b5096c4f0 100644
--- a/var/spack/packages/qt/package.py
+++ b/var/spack/packages/qt/package.py
@@ -43,9 +43,9 @@ class Qt(Package):
                   '-fast',
                   '-optimized-qmake',
                   '-no-pch',
-# phonon required for py-pyqt4
-#                  '-no-phonon',
-#                  '-no-phonon-backend',
+                  # phonon required for py-pyqt
+                  # '-no-phonon',
+                  # '-no-phonon-backend',
                   '-no-openvg')
         make()
         make("install")
-- 
cgit v1.2.3-70-g09d2


From ce011501f9b0184888ba2b6648fcf6d360f7c404 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 15 Feb 2015 23:02:21 -0800
Subject: Add R package.

---
 var/spack/packages/R/package.py | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 var/spack/packages/R/package.py

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")
-- 
cgit v1.2.3-70-g09d2


From 36579844d9f105b5c9182beed83a65bf0bb556a9 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 15 Feb 2015 23:02:36 -0800
Subject: Add Tcl/Tk packages.

---
 var/spack/packages/tcl/package.py | 22 ++++++++++++++++++++++
 var/spack/packages/tk/package.py  | 22 ++++++++++++++++++++++
 2 files changed, 44 insertions(+)
 create mode 100644 var/spack/packages/tcl/package.py
 create mode 100644 var/spack/packages/tk/package.py

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")
-- 
cgit v1.2.3-70-g09d2


From 65d60f92f5c479bdcf8b4cbfa244135a131d08f9 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 15 Feb 2015 23:02:51 -0800
Subject: qhull package.

---
 var/spack/packages/qhull/package.py | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 var/spack/packages/qhull/package.py

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")
-- 
cgit v1.2.3-70-g09d2


From b86eb695523c235371169d0139486bcae15a7948 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 15 Feb 2015 23:03:33 -0800
Subject: libgcrypt and libgpg-error packages.

---
 var/spack/packages/libgcrypt/package.py    | 19 +++++++++++++++++++
 var/spack/packages/libgpg-error/package.py | 17 +++++++++++++++++
 2 files changed, 36 insertions(+)
 create mode 100644 var/spack/packages/libgcrypt/package.py
 create mode 100644 var/spack/packages/libgpg-error/package.py

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")
-- 
cgit v1.2.3-70-g09d2


From 847ed8ad399973477a7889b6367911f10c56f6bf Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 15 Feb 2015 23:04:04 -0800
Subject: Add libxslt, cleanup libxml2.

---
 var/spack/packages/libxml2/package.py |  3 +++
 var/spack/packages/libxslt/package.py | 24 ++++++++++++++++++++++++
 2 files changed, 27 insertions(+)
 create mode 100644 var/spack/packages/libxslt/package.py

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")
-- 
cgit v1.2.3-70-g09d2


From 8aa3afcfde9cebd34fdb534141c258c214ae4132 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 15 Feb 2015 23:04:20 -0800
Subject: Python package cleanup.

- Added a number of dependencies to python packages.
- Python packages may still not build without some OS support.
- Example: Numpy needs ATLAS, and will use a system ATLAS install.
  - Atlas requires turning off CPU throttling to build.
  - can't do this as a regular user -- how to build ATLAS with Spack
  - currnetly relying on a system ATLAS install.
---
 var/spack/packages/py-libxml2/package.py          |  1 +
 var/spack/packages/py-matplotlib/package.py       |  6 +++++-
 var/spack/packages/py-pyside/package.py           |  1 -
 var/spack/packages/py-rpy2/package.py             |  2 ++
 var/spack/packages/py-scientificpython/package.py |  6 +++++-
 var/spack/packages/py-shiboken/package.py         | 19 +++++++++++++++++++
 6 files changed, 32 insertions(+), 3 deletions(-)

diff --git a/var/spack/packages/py-libxml2/package.py b/var/spack/packages/py-libxml2/package.py
index e645acb5dd..59005428e4 100644
--- a/var/spack/packages/py-libxml2/package.py
+++ b/var/spack/packages/py-libxml2/package.py
@@ -9,6 +9,7 @@ class PyLibxml2(Package):
 
     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
index 8b8684c563..f6b9c587fd 100644
--- a/var/spack/packages/py-matplotlib/package.py
+++ b/var/spack/packages/py-matplotlib/package.py
@@ -17,8 +17,12 @@ class PyMatplotlib(Package):
     depends_on('py-pytz')
     depends_on('py-nose')
     depends_on('py-numpy')
-    depends_on('qt')
 
+    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)
diff --git a/var/spack/packages/py-pyside/package.py b/var/spack/packages/py-pyside/package.py
index 1fd037d75f..c165d9b3bf 100644
--- a/var/spack/packages/py-pyside/package.py
+++ b/var/spack/packages/py-pyside/package.py
@@ -13,7 +13,6 @@ class PyPyside(Package):
     depends_on('py-setuptools')
     depends_on('qt@:4')
 
-
     def patch(self):
         """Undo PySide RPATH handling and add Spack RPATH."""
         # Add Spack's standard CMake args to the sub-builds.
diff --git a/var/spack/packages/py-rpy2/package.py b/var/spack/packages/py-rpy2/package.py
index 3817059911..dd0c0672af 100644
--- a/var/spack/packages/py-rpy2/package.py
+++ b/var/spack/packages/py-rpy2/package.py
@@ -10,5 +10,7 @@ class PyRpy2(Package):
     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
index 73600e6cb9..020d830703 100644
--- a/var/spack/packages/py-scientificpython/package.py
+++ b/var/spack/packages/py-scientificpython/package.py
@@ -1,7 +1,11 @@
 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."""
+    """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"
 
diff --git a/var/spack/packages/py-shiboken/package.py b/var/spack/packages/py-shiboken/package.py
index 47abe64e65..e900947939 100644
--- a/var/spack/packages/py-shiboken/package.py
+++ b/var/spack/packages/py-shiboken/package.py
@@ -15,6 +15,25 @@ class PyShiboken(Package):
     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.
+        filter_file(
+            r'OPTION_CMAKE,',
+            r'OPTION_CMAKE, ' + (
+                '"-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE", '
+                '"-DCMAKE_INSTALL_RPATH=%s",' % ':'.join(self.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,
-- 
cgit v1.2.3-70-g09d2


From 614c22fc1b1ac10c85ed9e27a1e59eeb88de0898 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 16 Feb 2015 12:41:22 -0800
Subject: Allow forced deactivation -- best effort unlinking

spack deactivate -f will unlink even if Spack thinks the package isn't enabled.
Made deactivate routines idempotent.
---
 lib/spack/llnl/util/link_tree.py     | 4 ++++
 lib/spack/spack/cmd/deactivate.py    | 7 +++++--
 lib/spack/spack/cmd/find.py          | 3 +++
 var/spack/packages/python/package.py | 5 +++--
 4 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/lib/spack/llnl/util/link_tree.py b/lib/spack/llnl/util/link_tree.py
index 4e4e48316e..4d778eca1e 100644
--- a/lib/spack/llnl/util/link_tree.py
+++ b/lib/spack/llnl/util/link_tree.py
@@ -175,6 +175,10 @@ class LinkTree(object):
         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)
 
diff --git a/lib/spack/spack/cmd/deactivate.py b/lib/spack/spack/cmd/deactivate.py
index fd13f051df..f37dfd79ed 100644
--- a/lib/spack/spack/cmd/deactivate.py
+++ b/lib/spack/spack/cmd/deactivate.py
@@ -30,6 +30,9 @@ import spack.cmd
 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(
         'spec', nargs=argparse.REMAINDER, help="spec of package extension to deactivate.")
 
@@ -44,7 +47,7 @@ def deactivate(parser, args):
     spack.db.get(specs[0])
 
     spec = spack.cmd.disambiguate_spec(specs[0])
-    if not spec.package.activated:
+    if not args.force and not spec.package.activated:
         tty.die("Package %s is not activated." % specs[0].short_spec)
 
-    spec.package.do_deactivate()
+    spec.package.do_deactivate(force=args.force)
diff --git a/lib/spack/spack/cmd/find.py b/lib/spack/spack/cmd/find.py
index f6f503afe5..dee1dfece7 100644
--- a/lib/spack/spack/cmd/find.py
+++ b/lib/spack/spack/cmd/find.py
@@ -122,5 +122,8 @@ def find(parser, args):
 
     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/var/spack/packages/python/package.py b/var/spack/packages/python/package.py
index fb875a7eeb..705d002e80 100644
--- a/var/spack/packages/python/package.py
+++ b/var/spack/packages/python/package.py
@@ -155,5 +155,6 @@ class Python(Package):
         super(Python, self).deactivate(ext_pkg, **args)
 
         exts = spack.install_layout.extension_map(self.spec)
-        del exts[ext_pkg.name]
-        self.write_easy_install_pth(exts)
+        if ext_pkg.name in exts:        # Make deactivate idempotent.
+            del exts[ext_pkg.name]
+            self.write_easy_install_pth(exts)
-- 
cgit v1.2.3-70-g09d2


From e6b2c2701184dd9128b729e11fc1f142272caa1d Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 16 Feb 2015 20:38:22 -0800
Subject: Factor out forking logic to build_environment.py.

---
 lib/spack/spack/build_environment.py | 56 ++++++++++++++++++++++++++++++++++++
 lib/spack/spack/package.py           | 39 +++++--------------------
 2 files changed, 63 insertions(+), 32 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index cabde7dc86..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
@@ -212,3 +213,58 @@ def setup_package(pkg):
     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/package.py b/lib/spack/spack/package.py
index c48816cb5b..5d04fed8ff 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -804,32 +804,21 @@ class Package(object):
         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:
@@ -852,10 +841,6 @@ class Package(object):
                         % (_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
@@ -865,24 +850,14 @@ 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 _sanity_check_install(self):
         installed = set(os.listdir(self.prefix))
         installed.difference_update(spack.install_layout.hidden_file_paths)
-- 
cgit v1.2.3-70-g09d2


From 13376efafc42c6eeb1bf0ad3b35f509924f1a6df Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 16 Feb 2015 21:53:34 -0800
Subject: Add package-specific rpath back to shiboken and pyside.

---
 var/spack/packages/py-pyside/package.py   | 13 ++++++++++---
 var/spack/packages/py-shiboken/package.py |  7 ++++++-
 2 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/var/spack/packages/py-pyside/package.py b/var/spack/packages/py-pyside/package.py
index c165d9b3bf..6583431124 100644
--- a/var/spack/packages/py-pyside/package.py
+++ b/var/spack/packages/py-pyside/package.py
@@ -1,5 +1,4 @@
 from spack import *
-import spack.package
 import os
 
 class PyPyside(Package):
@@ -9,25 +8,33 @@ class PyPyside(Package):
 
     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(self.rpath)),
+                '"-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'rpath_cmd\(pyside_path, srcpath\)',
+            r'^\s*rpath_cmd\(pyside_path, srcpath\)',
             r'#rpath_cmd(pyside_path, srcpath)',
             'pyside_postinstall.py')
 
diff --git a/var/spack/packages/py-shiboken/package.py b/var/spack/packages/py-shiboken/package.py
index e900947939..e4bf4ce07e 100644
--- a/var/spack/packages/py-shiboken/package.py
+++ b/var/spack/packages/py-shiboken/package.py
@@ -1,4 +1,5 @@
 from spack import *
+import os
 
 class PyShiboken(Package):
     """Shiboken generates bindings for C++ libraries using CPython source code."""
@@ -19,11 +20,15 @@ class PyShiboken(Package):
         """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(self.rpath)),
+                '"-DCMAKE_INSTALL_RPATH=%s",' % ':'.join(rpath)),
             'setup.py')
 
         # Shiboken tries to patch ELF files to remove RPATHs
-- 
cgit v1.2.3-70-g09d2


From 06d6b0b205095f849ace216aa51393b907cf821b Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 16 Feb 2015 21:53:55 -0800
Subject: More py-setuptools dependencies added.

---
 var/spack/packages/py-ipython/package.py    | 1 +
 var/spack/packages/py-mpi4py/package.py     | 1 +
 var/spack/packages/py-nose/package.py       | 1 +
 var/spack/packages/py-pylint/package.py     | 4 ++--
 var/spack/packages/py-virtualenv/package.py | 1 +
 5 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/var/spack/packages/py-ipython/package.py b/var/spack/packages/py-ipython/package.py
index 731e661dfd..907ea9edcd 100644
--- a/var/spack/packages/py-ipython/package.py
+++ b/var/spack/packages/py-ipython/package.py
@@ -9,6 +9,7 @@ class PyIpython(Package):
 
     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-mpi4py/package.py b/var/spack/packages/py-mpi4py/package.py
index fdea340dc2..8001689a18 100644
--- a/var/spack/packages/py-mpi4py/package.py
+++ b/var/spack/packages/py-mpi4py/package.py
@@ -7,6 +7,7 @@ class PyMpi4py(Package):
 
     version('1.3.1', 'dbe9d22bdc8ed965c23a7ceb6f32fc3c')
     extends('python')
+    depends_on('py-setuptools')
     depends_on('mpi')
 
     def install(self, spec, prefix):
diff --git a/var/spack/packages/py-nose/package.py b/var/spack/packages/py-nose/package.py
index 6df84e831d..b902a35fbb 100644
--- a/var/spack/packages/py-nose/package.py
+++ b/var/spack/packages/py-nose/package.py
@@ -10,6 +10,7 @@ class PyNose(Package):
     version('1.3.4', '6ed7169887580ddc9a8e16048d38274d')
 
     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
index ebde861f94..7a6ee7dbbc 100644
--- a/var/spack/packages/py-pylint/package.py
+++ b/var/spack/packages/py-pylint/package.py
@@ -8,9 +8,9 @@ class PyPylint(Package):
 
     version('1.4.1', 'df7c679bdcce5019389038847e4de622')
 
-#    extends('python')
-    extends('python', ignore=lambda f:re.match(r"site.py*", f))
+    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-virtualenv/package.py b/var/spack/packages/py-virtualenv/package.py
index c1b359e164..9d94c2dcda 100644
--- a/var/spack/packages/py-virtualenv/package.py
+++ b/var/spack/packages/py-virtualenv/package.py
@@ -9,6 +9,7 @@ class PyVirtualenv(Package):
     version('1.11.6', 'f61cdd983d2c4e6aeabb70b1060d6f49')
 
     extends('python')
+    depends_on('py-setuptools')
 
     def clean(self):
         if os.path.exists('build'):
-- 
cgit v1.2.3-70-g09d2


From 67db8ddca8ac7ab9adeb827a7dadd34a385b2b6b Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 17 Feb 2015 00:21:15 -0800
Subject: Factor ignore logic into a predicate builder.

---
 lib/spack/llnl/util/lang.py          | 31 +++++++++++++++++++++++++++++++
 var/spack/packages/python/package.py | 25 +++++++++++--------------
 2 files changed, 42 insertions(+), 14 deletions(-)

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/var/spack/packages/python/package.py b/var/spack/packages/python/package.py
index 705d002e80..31a12ea653 100644
--- a/var/spack/packages/python/package.py
+++ b/var/spack/packages/python/package.py
@@ -1,6 +1,7 @@
 import os
 import re
 from contextlib import closing
+from llnl.util.lang import match_predicate
 
 from spack import *
 import spack
@@ -85,23 +86,19 @@ class Python(Package):
 
     def python_ignore(self, ext_pkg, args):
         """Add some ignore files to activate/deactivate args."""
-        orig_ignore = args.get('ignore', lambda f: False)
+        ignore_arg = args.get('ignore', lambda f: False)
 
-        def ignore(filename):
-            # Always ignore easy-install.pth, as it needs to be merged.
-            patterns = [r'easy-install\.pth$']
+        # Always ignore easy-install.pth, as it needs to be merged.
+        patterns = [r'easy-install\.pth$']
 
-            # 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$')
+        # Ignore pieces of setuptools installed by other packages.
+        if ext_pkg.name != 'py-setuptools':
+            patterns.append(r'/site\.pyc?$')
+            patterns.append(r'setuptools\.pth')
+            patterns.append(r'bin/easy_install[^/]*$')
+            patterns.append(r'setuptools.*egg$')
 
-            return (any(re.search(p, filename) for p in patterns) or
-                    orig_ignore(filename))
-
-        return ignore
+        return match_predicate(ignore_arg, patterns)
 
 
     def write_easy_install_pth(self, exts):
-- 
cgit v1.2.3-70-g09d2


From 57f331e2acf75c5bf4c464d0df888fd882295a68 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 17 Feb 2015 00:22:18 -0800
Subject: Ignore conflicting nose tests in py-nose and py-matplotlib.

---
 var/spack/packages/py-matplotlib/package.py | 3 ++-
 var/spack/packages/py-nose/package.py       | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/var/spack/packages/py-matplotlib/package.py b/var/spack/packages/py-matplotlib/package.py
index f6b9c587fd..04037f004e 100644
--- a/var/spack/packages/py-matplotlib/package.py
+++ b/var/spack/packages/py-matplotlib/package.py
@@ -8,7 +8,8 @@ class PyMatplotlib(Package):
 
     version('1.4.2', '7d22efb6cce475025733c50487bd8898')
 
-    extends('python')
+    extends('python', ignore=r'bin/nosetests.*$')
+
     depends_on('py-pyside')
     depends_on('py-ipython')
     depends_on('py-pyparsing')
diff --git a/var/spack/packages/py-nose/package.py b/var/spack/packages/py-nose/package.py
index b902a35fbb..155019289d 100644
--- a/var/spack/packages/py-nose/package.py
+++ b/var/spack/packages/py-nose/package.py
@@ -9,7 +9,7 @@ class PyNose(Package):
 
     version('1.3.4', '6ed7169887580ddc9a8e16048d38274d')
 
-    extends('python')
+    extends('python', ignore=r'bin/nosetests.*$')
     depends_on('py-setuptools')
 
     def install(self, spec, prefix):
-- 
cgit v1.2.3-70-g09d2


From d800c23cecd9c87b17991411512e3aa42855815d Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 17 Feb 2015 00:24:58 -0800
Subject: Better activate/deactivate logic.

spack activate
  - now activates dependency extensions
  - ensures dependencies are activated in the python installation.
  - -f/--force option still allows the old activate behavior.

spack deactivate
  - checks for dependents before deactivating (like uninstall)
  - deactivate -a/--all <extension> will deactviate a package and ALL
    of its dependency extensions.
  - deactivate -a/--all <extendee> activates all extensions of <extendee>
    e.g.: spack deactivate -a python
  - deactivate -f/--force option allows removing regardless of dependents.
    - deactivate -f can be run EVEN if a package is not activated.
    - allows for clenup of activations gone wrong.
---
 lib/spack/spack/cmd/activate.py     |  6 +++++
 lib/spack/spack/cmd/deactivate.py   | 54 ++++++++++++++++++++++++++++++++++---
 lib/spack/spack/cmd/find.py         |  2 +-
 lib/spack/spack/directory_layout.py |  8 +++---
 lib/spack/spack/hooks/extensions.py |  2 +-
 lib/spack/spack/package.py          | 42 ++++++++++++++++++++++-------
 6 files changed, 95 insertions(+), 19 deletions(-)

diff --git a/lib/spack/spack/cmd/activate.py b/lib/spack/spack/cmd/activate.py
index c1e23852d6..71eca4f453 100644
--- a/lib/spack/spack/cmd/activate.py
+++ b/lib/spack/spack/cmd/activate.py
@@ -30,6 +30,9 @@ 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.")
 
@@ -44,6 +47,9 @@ def activate(parser, args):
     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)
 
diff --git a/lib/spack/spack/cmd/deactivate.py b/lib/spack/spack/cmd/deactivate.py
index f37dfd79ed..bfec618c8e 100644
--- a/lib/spack/spack/cmd/deactivate.py
+++ b/lib/spack/spack/cmd/deactivate.py
@@ -24,8 +24,10 @@
 ##############################################################################
 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."
 
@@ -33,6 +35,10 @@ 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.")
 
@@ -42,12 +48,52 @@ def deactivate(parser, args):
     if len(specs) != 1:
         tty.die("deactivate requires one spec.  %d given." % len(specs))
 
-    # TODO: remove this hack when DAG info is stored in dir layout.
+    # 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])
-    if not args.force and not spec.package.activated:
-        tty.die("Package %s is not activated." % specs[0].short_spec)
+    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)
+        spec.package.do_deactivate(force=args.force)
diff --git a/lib/spack/spack/cmd/find.py b/lib/spack/spack/cmd/find.py
index dee1dfece7..70b10edb4e 100644
--- a/lib/spack/spack/cmd/find.py
+++ b/lib/spack/spack/cmd/find.py
@@ -85,7 +85,7 @@ def display_specs(specs, **kwargs):
 
         elif mode == 'deps':
             for spec in specs:
-                print spec.tree(indent=4, format='$_$@$+', color=True),
+                print spec.tree(indent=4, format='$_$@$+$#', color=True),
 
         elif mode in ('short', 'long'):
             fmt = '$-_$@$+'
diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index 5b80e93d6b..b2cf5dc801 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -371,7 +371,7 @@ class SpecHashDirectoryLayout(DirectoryLayout):
         _check_concrete(ext_spec)
 
         # Check whether it's already installed or if it's a conflict.
-        exts = self.extension_map(spec)
+        exts = self._extension_map(spec)
         self.check_extension_conflict(spec, ext_spec)
 
         # do the actual adding.
@@ -384,7 +384,7 @@ class SpecHashDirectoryLayout(DirectoryLayout):
         _check_concrete(ext_spec)
 
         # Make sure it's installed before removing.
-        exts = self.extension_map(spec)
+        exts = self._extension_map(spec)
         self.check_activated(spec, ext_spec)
 
         # do the actual removing.
@@ -450,10 +450,10 @@ class ExtensionConflictError(DirectoryLayoutError):
 
 
 class NoSuchExtensionError(DirectoryLayoutError):
-    """Raised when an extension isn't there on remove."""
+    """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 installed."% (
+            "%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/extensions.py b/lib/spack/spack/hooks/extensions.py
index 9d6fa23d03..cf87a78c8c 100644
--- a/lib/spack/spack/hooks/extensions.py
+++ b/lib/spack/spack/hooks/extensions.py
@@ -33,4 +33,4 @@ def pre_uninstall(pkg):
 
     if pkg.is_extension:
         if pkg.activated:
-            pkg.do_deactivate()
+            pkg.do_deactivate(force=True)
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 5d04fed8ff..bc8541a184 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -529,11 +529,8 @@ class Package(object):
 
     @property
     def activated(self):
-        if not self.spec.concrete:
-            raise ValueError("Only concrete package extensions can be activated.")
         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)
 
@@ -956,20 +953,33 @@ class Package(object):
             raise ValueError("%s does not extend %s!" % (self.name, self.extendee.name))
 
 
-    def do_activate(self):
+    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.short_spec))
+                % (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
 
 
     def activate(self, extension, **kwargs):
@@ -994,15 +1004,21 @@ class Package(object):
 
     def do_deactivate(self, **kwargs):
         """Called on the extension to invoke extendee's deactivate() method."""
-        force = kwargs.get('force', False)
-
         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
@@ -1011,7 +1027,7 @@ class Package(object):
             spack.install_layout.remove_extension(self.extendee_spec, self.spec)
 
         tty.msg("Deactivated extension %s for %s."
-                % (self.spec.short_spec, self.extendee_spec.short_spec))
+                % (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
 
 
     def deactivate(self, extension, **kwargs):
@@ -1236,7 +1252,15 @@ class NoURLError(PackageError):
             "Package %s has no version with a URL." % cls.__name__)
 
 
-class ExtensionConflictError(PackageError):
+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)
-- 
cgit v1.2.3-70-g09d2