re-merged mainline develop

27 files changed, 1248 insertions, 809 deletions

diff --git a/.flake8 b/.flake8
index a1e2fcc1f8..12ae2efa80 100644
--- a/.flake8
+++ b/.flake8
@@ -8,6 +8,9 @@
 # - E221: multiple spaces before operator
 # - E241: multiple spaces after ‘,’
 #
+# Let people use terse Python features:
+# - E731 : lambda expressions
+#
 # Spack allows wildcard imports:
 # - F403: disable wildcard import
 #
@@ -16,5 +19,5 @@
 # - F999: name name be undefined or undefined from star imports.
 #
 [flake8]
-ignore = E221,E241,F403,F821,F999
+ignore = E221,E241,E731,F403,F821,F999
 max-line-length = 79
diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst
index 15db2f7a16..2eed9dddd4 100644
--- a/lib/spack/docs/basic_usage.rst
+++ b/lib/spack/docs/basic_usage.rst
@@ -102,8 +102,8 @@ that the packages is installed:
    ==> adept-utils is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/adept-utils@1.0-5adef8da.
    ==> Trying to fetch from https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
    ######################################################################## 100.0%
-   ==> Staging archive: /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7=chaos_5_x86_64_ib-59f6ad23/mpileaks-1.0.tar.gz
-   ==> Created stage in /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7=chaos_5_x86_64_ib-59f6ad23.
+   ==> Staging archive: /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=chaos_5_x86_64_ib-59f6ad23/mpileaks-1.0.tar.gz
+   ==> Created stage in /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=chaos_5_x86_64_ib-59f6ad23.
    ==> No patches needed for mpileaks.
    ==> Building mpileaks.
 
@@ -132,10 +132,10 @@ sites, as installing a version that one user needs will not disrupt
 existing installations for other users.
 
 In addition to different versions, Spack can customize the compiler,
-compile-time options (variants), and platform (for cross compiles) of
-an installation.  Spack is unique in that it can also configure the
-*dependencies* a package is built with.  For example, two
-configurations of the same version of a package, one built with boost
+compile-time options (variants), compiler flags, and platform (for
+cross compiles) of an installation.  Spack is unique in that it can
+also configure the *dependencies* a package is built with.  For example,
+two configurations of the same version of a package, one built with boost
 1.39.0, and the other version built with version 1.43.0, can coexist.
 
 This can all be done on the command line using the *spec* syntax.
@@ -246,6 +246,12 @@ Packages are divided into groups according to their architecture and
 compiler.  Within each group, Spack tries to keep the view simple, and
 only shows the version of installed packages.
 
+``spack find`` can filter the package list based on the package name, spec, or
+a number of properties of their installation status.  For example, missing
+dependencies of a spec can be shown with ``-m``, packages which were
+explicitly installed with ``spack install <package>`` can be singled out with
+``-e`` and those which have been pulled in only as dependencies with ``-E``.
+
 In some cases, there may be different configurations of the *same*
 version of a package installed.  For example, there are two
 installations of of ``libdwarf@20130729`` above.  We can look at them
@@ -328,6 +334,11 @@ of libelf would look like this:
    -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
    libdwarf@20130729-d9b90962
 
+We can also search for packages that have a certain attribute. For example,
+``spack find -l libdwarf +debug`` will show only installations of libdwarf
+with the 'debug' compile-time option enabled, while ``spack find -l +debug``
+will find every installed package with a 'debug' compile-time option enabled.
+
 The full spec syntax is discussed in detail in :ref:`sec-specs`.
 
 
@@ -457,6 +468,26 @@ For compilers, like ``clang``, that do not support Fortran, put
 Once you save the file, the configured compilers will show up in the
 list displayed by ``spack compilers``.
 
+You can also add compiler flags to manually configured compilers. The
+valid flags are ``cflags``, ``cxxflags``, ``fflags``, ``cppflags``,
+``ldflags``, and ``ldlibs``. For example,::
+
+    ...
+    chaos_5_x86_64_ib:
+      ...
+      intel@15.0.0:
+          cc: /usr/local/bin/icc-15.0.024-beta
+          cxx: /usr/local/bin/icpc-15.0.024-beta
+          f77: /usr/local/bin/ifort-15.0.024-beta
+          fc: /usr/local/bin/ifort-15.0.024-beta
+          cppflags: -O3 -fPIC
+      ...
+
+These flags will be treated by spack as if they were enterred from
+the command line each time this compiler is used. The compiler wrappers
+then inject those flags into the compiler command. Compiler flags
+enterred from the command line will be discussed in more detail in the
+following section.
 
 .. _sec-specs:
 
@@ -474,7 +505,7 @@ the full syntax of specs.
 
 Here is an example of a much longer spec than we've seen thus far::
 
-   mpileaks @1.2:1.4 %gcc@4.7.5 +debug -qt =bgqos_0 ^callpath @1.1 %gcc@4.7.2
+   mpileaks @1.2:1.4 %gcc@4.7.5 +debug -qt arch=bgq_os ^callpath @1.1 %gcc@4.7.2
 
 If provided to ``spack install``, this will install the ``mpileaks``
 library at some version between ``1.2`` and ``1.4`` (inclusive),
@@ -492,8 +523,12 @@ More formally, a spec consists of the following pieces:
 * ``%`` Optional compiler specifier, with an optional compiler version
   (``gcc`` or ``gcc@4.7.3``)
 * ``+`` or ``-`` or ``~`` Optional variant specifiers (``+debug``,
-  ``-qt``, or ``~qt``)
-* ``=`` Optional architecture specifier (``bgqos_0``)
+  ``-qt``, or ``~qt``) for boolean variants
+* ``name=<value>`` Optional variant specifiers that are not restricted to
+boolean variants
+* ``name=<value>`` Optional compiler flag specifiers. Valid flag names are
+``cflags``, ``cxxflags``, ``fflags``, ``cppflags``, ``ldflags``, and ``ldlibs``.
+* ``arch=<value>`` Optional architecture specifier (``arch=bgq_os``)
 * ``^`` Dependency specs (``^callpath@1.1``)
 
 There are two things to notice here.  The first is that specs are
@@ -573,7 +608,7 @@ compilers, variants, and architectures just like any other spec.
 Specifiers are associated with the nearest package name to their left.
 For example, above, ``@1.1`` and ``%gcc@4.7.2`` associates with the
 ``callpath`` package, while ``@1.2:1.4``, ``%gcc@4.7.5``, ``+debug``,
-``-qt``, and ``=bgqos_0`` all associate with the ``mpileaks`` package.
+``-qt``, and ``arch=bgq_os`` all associate with the ``mpileaks`` package.
 
 In the diagram above, ``mpileaks`` depends on ``mpich`` with an
 unspecified version, but packages can depend on other packages with
@@ -629,22 +664,25 @@ based on site policies.
 Variants
 ~~~~~~~~~~~~~~~~~~~~~~~
 
-.. Note::
-
-   Variants are not yet supported, but will be in the next Spack
-   release (0.9), due in Q2 2015.
-
-Variants are named options associated with a particular package, and
-they can be turned on or off.  For example, above, supplying
-``+debug`` causes ``mpileaks`` to be built with debug flags.  The
-names of particular variants available for a package depend on what
-was provided by the package author.  ``spack info <package>`` will
+Variants are named options associated with a particular package. They are
+optional, as each package must provide default values for each variant it
+makes available. Variants can be specified using
+a flexible parameter syntax ``name=<value>``. For example,
+``spack install libelf debug=True`` will install libelf build with debug
+flags. The names of particular variants available for a package depend on
+what was provided by the package author. ``spack into <package>`` will
 provide information on what build variants are available.
 
-Depending on the package a variant may be on or off by default.  For
-``mpileaks`` here, ``debug`` is off by default, and we turned it on
-with ``+debug``.  If a package is on by default you can turn it off by
-either adding ``-name`` or ``~name`` to the spec.
+For compatibility with earlier versions, variants which happen to be
+boolean in nature can be specified by a syntax that represents turning
+options on and off. For example, in the previous spec we could have
+supplied ``libelf +debug`` with the same effect of enabling the debug
+compile time option for the libelf package.
+
+Depending on the package a variant may have any default value.  For
+``libelf`` here, ``debug`` is ``False`` by default, and we turned it on
+with ``debug=True`` or ``+debug``.  If a package is ``True`` by default
+you can turn it off by either adding ``-name`` or ``~name`` to the spec.
 
 There are two syntaxes here because, depending on context, ``~`` and
 ``-`` may mean different things.  In most shells, the following will
@@ -656,7 +694,7 @@ result in the shell performing home directory substitution:
    mpileaks~debug    # use this instead
 
 If there is a user called ``debug``, the ``~`` will be incorrectly
-expanded.  In this situation, you would want to write ``mpileaks
+expanded.  In this situation, you would want to write ``libelf
 -debug``.  However, ``-`` can be ambiguous when included after a
 package name without spaces:
 
@@ -671,12 +709,35 @@ package, not a request for ``mpileaks`` built without ``debug``
 options.  In this scenario, you should write ``mpileaks~debug`` to
 avoid ambiguity.
 
-When spack normalizes specs, it prints them out with no spaces and
-uses only ``~`` for disabled variants.  We allow ``-`` and spaces on
-the command line is provided for convenience and legibility.
+When spack normalizes specs, it prints them out with no spaces boolean
+variants using the backwards compatibility syntax and uses only ``~``
+for disabled boolean variants.  We allow ``-`` and spaces on the command
+line is provided for convenience and legibility.
 
 
-Architecture specifier
+Compiler Flags
+~~~~~~~~~~~~~~~~~~~~~~~
+
+Compiler flags are specified using the same syntax as non-boolean variants,
+but fulfill a different purpose. While the function of a variant is set by
+the package, compiler flags are used by the compiler wrappers to inject
+flags into the compile line of the build. Additionally, compiler flags are
+inherited by dependencies. ``spack install libdwarf cppflags=\"-g\"`` will
+install both libdwarf and libelf with the ``-g`` flag injected into their
+compile line.
+
+Notice that the value of the compiler flags must be escape quoted on the
+command line. From within python files, the same spec would be specified
+``libdwarf cppflags="-g"``. This is necessary because of how the shell
+handles the quote symbols.
+
+The six compiler flags are injected in the order of implicit make commands
+in gnu autotools. If all flags are set, the order is
+``$cppflags $cflags|$cxxflags $ldflags command $ldlibs`` for C and C++ and
+``$fflags $cppflags $ldflags command $ldlibs`` for fortran.
+
+
+Architecture specifiers
 ~~~~~~~~~~~~~~~~~~~~~~~
 
 .. Note::
@@ -684,12 +745,9 @@ Architecture specifier
    Architecture specifiers are part of specs but are not yet
    functional. They will be in Spack version 1.0, due in Q3 2015.
 
-The architecture specifier starts with a ``=`` and also comes after
-some package name within a spec.  It allows a user to specify a
-particular architecture for the package to be built.  This is mostly
-used for architectures that need cross-compilation, and in most cases,
-users will not need to specify the architecture when they install a
-package.
+The architecture specifier looks identical to a variant specifier for a
+non-boolean variant. The architecture can be specified only using the
+reserved name ``arch`` (``arch=bgq_os``).
 
 
 .. _sec-virtual-dependencies:
@@ -767,6 +825,23 @@ any MPI implementation will do.  If another package depends on
 error.  Likewise, if you try to plug in some package that doesn't
 provide MPI, Spack will raise an error.
 
+Specifying Specs by Hash
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Complicated specs can become cumbersome to enter on the command line,
+especially when many of the qualifications are necessary to
+distinguish between similar installs, for example when using the
+``uninstall`` command. To avoid this, when referencing an existing spec,
+Spack allows you to reference specs by their hash. We previously
+discussed the spec hash that Spack computes. In place of a spec in any
+command, substitute ``/<hash>`` where ``<hash>`` is any amount from
+the beginning of a spec hash. If the given spec hash is sufficient
+to be unique, Spack will replace the reference with the spec to which
+it refers. Otherwise, it will prompt for a more qualified hash.
+
+Note that this will not work to reinstall a depencency uninstalled by
+``spack uninstall -f``.
+
 .. _spack-providers:
 
 ``spack providers``
@@ -996,8 +1071,8 @@ than one installed package matches it), then Spack will warn you:
 
    $ spack load libelf
    ==> Error: Multiple matches for spec libelf.  Choose one:
-   libelf@0.8.13%gcc@4.4.7=chaos_5_x86_64_ib
-   libelf@0.8.13%intel@15.0.0=chaos_5_x86_64_ib
+   libelf@0.8.13%gcc@4.4.7 arch=chaos_5_x86_64_ib
+   libelf@0.8.13%intel@15.0.0 arch=chaos_5_x86_64_ib
 
 You can either type the ``spack load`` command again with a fully
 qualified argument, or you can add just enough extra constraints to
@@ -1276,7 +1351,7 @@ You can find extensions for your Python installation like this:
 .. code-block:: sh
 
    $ spack extensions python
-   ==> python@2.7.8%gcc@4.4.7=chaos_5_x86_64_ib-703c7a96
+   ==> python@2.7.8%gcc@4.4.7 arch=chaos_5_x86_64_ib-703c7a96
    ==> 36 extensions:
    geos          py-ipython     py-pexpect    py-pyside            py-sip
    py-basemap    py-libxml2     py-pil        py-pytz              py-six
@@ -1366,9 +1441,9 @@ installation:
 .. code-block:: sh
 
    $ spack activate py-numpy
-   ==> Activated extension py-setuptools@11.3.1%gcc@4.4.7=chaos_5_x86_64_ib-3c74eb69 for python@2.7.8%gcc@4.4.7.
-   ==> Activated extension py-nose@1.3.4%gcc@4.4.7=chaos_5_x86_64_ib-5f70f816 for python@2.7.8%gcc@4.4.7.
-   ==> Activated extension py-numpy@1.9.1%gcc@4.4.7=chaos_5_x86_64_ib-66733244 for python@2.7.8%gcc@4.4.7.
+   ==> Activated extension py-setuptools@11.3.1%gcc@4.4.7 arch=chaos_5_x86_64_ib-3c74eb69 for python@2.7.8%gcc@4.4.7.
+   ==> Activated extension py-nose@1.3.4%gcc@4.4.7 arch=chaos_5_x86_64_ib-5f70f816 for python@2.7.8%gcc@4.4.7.
+   ==> Activated extension py-numpy@1.9.1%gcc@4.4.7 arch=chaos_5_x86_64_ib-66733244 for python@2.7.8%gcc@4.4.7.
 
 Several things have happened here.  The user requested that
 ``py-numpy`` be activated in the ``python`` installation it was built
@@ -1383,7 +1458,7 @@ packages listed as activated:
 .. code-block:: sh
 
    $ spack extensions python
-   ==> python@2.7.8%gcc@4.4.7=chaos_5_x86_64_ib-703c7a96
+   ==> python@2.7.8%gcc@4.4.7  arch=chaos_5_x86_64_ib-703c7a96
    ==> 36 extensions:
    geos          py-ipython     py-pexpect    py-pyside            py-sip
    py-basemap    py-libxml2     py-pil        py-pytz              py-six
@@ -1431,7 +1506,7 @@ dependencies, you can use ``spack activate -f``:
 .. code-block:: sh
 
    $ spack activate -f py-numpy
-   ==> Activated extension py-numpy@1.9.1%gcc@4.4.7=chaos_5_x86_64_ib-66733244 for python@2.7.8%gcc@4.4.7.
+   ==> Activated extension py-numpy@1.9.1%gcc@4.4.7 arch=chaos_5_x86_64_ib-66733244 for python@2.7.8%gcc@4.4.7.
 
 .. _spack-deactivate:
 
diff --git a/lib/spack/docs/site_configuration.rst b/lib/spack/docs/configuration.rst
index 3abfa21a9d..c613071c65 100644
--- a/lib/spack/docs/site_configuration.rst
+++ b/lib/spack/docs/configuration.rst
@@ -1,6 +1,6 @@
-.. _site-configuration:
+.. _configuration:
 
-Site configuration
+Configuration
 ===================================
 
 .. _temp-space:
@@ -55,7 +55,7 @@ directory is.
 
 
 External Packages
-~~~~~~~~~~~~~~~~~~~~~
+----------------------------
 Spack can be configured to use externally-installed
 packages rather than building its own packages. This may be desirable
 if machines ship with system packages, such as a customized MPI
@@ -70,15 +70,15 @@ directory. Here's an example of an external configuration:
    packages:
       openmpi:
          paths:
-            openmpi@1.4.3%gcc@4.4.7=chaos_5_x86_64_ib: /opt/openmpi-1.4.3
-            openmpi@1.4.3%gcc@4.4.7=chaos_5_x86_64_ib+debug: /opt/openmpi-1.4.3-debug
-            openmpi@1.6.5%intel@10.1=chaos_5_x86_64_ib: /opt/openmpi-1.6.5-intel
+            openmpi@1.4.3%gcc@4.4.7 arch=chaos_5_x86_64_ib: /opt/openmpi-1.4.3
+            openmpi@1.4.3%gcc@4.4.7 arch=chaos_5_x86_64_ib+debug: /opt/openmpi-1.4.3-debug
+            openmpi@1.6.5%intel@10.1 arch=chaos_5_x86_64_ib: /opt/openmpi-1.6.5-intel
 
 This example lists three installations of OpenMPI, one built with gcc,
 one built with gcc and debug information, and another built with Intel.
 If Spack is asked to build a package that uses one of these MPIs as a
 dependency, it will use the the pre-installed OpenMPI in
-the given directory.  
+the given directory.
 
 Each ``packages.yaml`` begins with a ``packages:`` token, followed
 by a list of package names.  To specify externals, add a ``paths``
@@ -108,9 +108,9 @@ be:
   packages:
     openmpi:
       paths:
-        openmpi@1.4.3%gcc@4.4.7=chaos_5_x86_64_ib: /opt/openmpi-1.4.3
-        openmpi@1.4.3%gcc@4.4.7=chaos_5_x86_64_ib+debug: /opt/openmpi-1.4.3-debug
-        openmpi@1.6.5%intel@10.1=chaos_5_x86_64_ib: /opt/openmpi-1.6.5-intel                
+        openmpi@1.4.3%gcc@4.4.7 arch=chaos_5_x86_64_ib: /opt/openmpi-1.4.3
+        openmpi@1.4.3%gcc@4.4.7 arch=chaos_5_x86_64_ib+debug: /opt/openmpi-1.4.3-debug
+        openmpi@1.6.5%intel@10.1 arch=chaos_5_x86_64_ib: /opt/openmpi-1.6.5-intel
       buildable: False
 
 The addition of the ``buildable`` flag tells Spack that it should never build
@@ -118,13 +118,73 @@ its own version of OpenMPI, and it will instead always rely on a pre-built
 OpenMPI.  Similar to ``paths``, ``buildable`` is specified as a property under
 a package name.
 
-The ``buildable`` does not need to be paired with external packages.  
-It could also be used alone to forbid packages that may be 
+The ``buildable`` does not need to be paired with external packages.
+It could also be used alone to forbid packages that may be
 buggy or otherwise undesirable.
 
 
+Concretization Preferences
+--------------------------------
+
+Spack can be configured to prefer certain compilers, package
+versions, depends_on, and variants during concretization.
+The preferred configuration can be controlled via the
+``~/.spack/packages.yaml`` file for user configuations, or the
+``etc/spack/packages.yaml`` site configuration.
+
+
+Here's an example packages.yaml file that sets preferred packages:
+
+.. code-block:: sh
+
+    packages:
+      dyninst:
+        compiler: [gcc@4.9]
+        variants: +debug
+      gperftools:
+        version: [2.2, 2.4, 2.3]
+      all:
+        compiler: [gcc@4.4.7, gcc@4.6:, intel, clang, pgi]
+        providers:
+          mpi: [mvapich, mpich, openmpi]
+
+
+At a high level, this example is specifying how packages should be
+concretized.  The dyninst package should prefer using gcc 4.9 and
+be built with debug options.  The gperftools package should prefer version
+2.2 over 2.4.  Every package on the system should prefer mvapich for
+its MPI and gcc 4.4.7 (except for Dyninst, which overrides this by preferring gcc 4.9).
+These options are used to fill in implicit defaults.  Any of them can be overwritten
+on the command line if explicitly requested.
+
+Each packages.yaml file begins with the string ``packages:`` and
+package names are specified on the next level. The special string ``all``
+applies settings to each package. Underneath each package name is
+one or more components: ``compiler``, ``variants``, ``version``,
+or ``providers``.  Each component has an ordered list of spec
+``constraints``, with earlier entries in the list being preferred over
+later entries.
+
+Sometimes a package installation may have constraints that forbid
+the first concretization rule, in which case Spack will use the first
+legal concretization rule.  Going back to the example, if a user
+requests gperftools 2.3 or later, then Spack will install version 2.4
+as the 2.4 version of gperftools is preferred over 2.3.
+
+An explicit concretization rule in the preferred section will always
+take preference over unlisted concretizations.  In the above example,
+xlc isn't listed in the compiler list.  Every listed compiler from
+gcc to pgi will thus be preferred over the xlc compiler.
+
+The syntax for the ``provider`` section differs slightly from other
+concretization rules.  A provider lists a value that packages may
+``depend_on`` (e.g, mpi) and a list of rules for fulfilling that
+dependency.
+
+
+
 Profiling
-~~~~~~~~~~~~~~~~~~~~~
+------------------
 
 Spack has some limited built-in support for profiling, and can report
 statistics using standard Python timing tools.  To use this feature,
@@ -133,7 +193,7 @@ supply ``-p`` to Spack on the command line, before any subcommands.
 .. _spack-p:
 
 ``spack -p``
-^^^^^^^^^^^^^^^^^^
+~~~~~~~~~~~~~~~~~
 
 ``spack -p`` output looks like this:
 
diff --git a/lib/spack/docs/features.rst b/lib/spack/docs/features.rst
index 0998ba8da4..27a3b4b435 100644
--- a/lib/spack/docs/features.rst
+++ b/lib/spack/docs/features.rst
@@ -31,14 +31,21 @@ platform, all on the command line.
    # Specify a compiler (and its version), with %
    $ spack install mpileaks@1.1.2 %gcc@4.7.3
 
-   # Add special compile-time options with +
+   # Add special compile-time options by name
+   $ spack install mpileaks@1.1.2 %gcc@4.7.3 debug=True
+
+   # Add special boolean compile-time options with +
    $ spack install mpileaks@1.1.2 %gcc@4.7.3 +debug
 
-   # Cross-compile for a different architecture with =
-   $ spack install mpileaks@1.1.2 =bgqos_0
+   # Add compiler flags using the conventional names
+   $ spack install mpileaks@1.1.2 %gcc@4.7.3 cppflags=\"-O3 -floop-block\"
+
+   # Cross-compile for a different architecture with arch=
+   $ spack install mpileaks@1.1.2 arch=bgqos_0
 
-Users can specify as many or few options as they care about.  Spack
-will fill in the unspecified values with sensible defaults.
+Users can specify as many or few options as they care about. Spack
+will fill in the unspecified values with sensible defaults. The two listed
+syntaxes for variants are identical when the value is boolean.
 
 
 Customize dependencies
diff --git a/lib/spack/docs/index.rst b/lib/spack/docs/index.rst
index d6ce52b747..98ed9ff0fe 100644
--- a/lib/spack/docs/index.rst
+++ b/lib/spack/docs/index.rst
@@ -47,7 +47,7 @@ Table of Contents
    basic_usage
    packaging_guide
    mirrors
-   site_configuration
+   configuration
    developer_guide
    command_index
    package_list
diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst
index 650e0ee3b2..1f83f611b0 100644
--- a/lib/spack/docs/packaging_guide.rst
+++ b/lib/spack/docs/packaging_guide.rst
@@ -1221,11 +1221,13 @@ just as easily provide a version range:
 
    depends_on("libelf@0.8.2:0.8.4:")
 
-Or a requirement for a particular variant:
+Or a requirement for a particular variant or compiler flags:
 
 .. code-block:: python
 
    depends_on("libelf@0.8+debug")
+   depends_on('libelf debug=True')
+   depends_on('libelf cppflags="-fPIC")
 
 Both users *and* package authors can use the same spec syntax to refer
 to different package configurations.  Users use the spec syntax on the
@@ -1623,21 +1625,21 @@ the user runs ``spack install`` and the time the ``install()`` method
 is called.  The concretized version of the spec above might look like
 this::
 
-   mpileaks@2.3%gcc@4.7.3=linux-ppc64
-       ^callpath@1.0%gcc@4.7.3+debug=linux-ppc64
-           ^dyninst@8.1.2%gcc@4.7.3=linux-ppc64
-               ^libdwarf@20130729%gcc@4.7.3=linux-ppc64
-                   ^libelf@0.8.11%gcc@4.7.3=linux-ppc64
-           ^mpich@3.0.4%gcc@4.7.3=linux-ppc64
+   mpileaks@2.3%gcc@4.7.3 arch=linux-ppc64
+       ^callpath@1.0%gcc@4.7.3+debug arch=linux-ppc64
+           ^dyninst@8.1.2%gcc@4.7.3 arch=linux-ppc64
+               ^libdwarf@20130729%gcc@4.7.3 arch=linux-ppc64
+                   ^libelf@0.8.11%gcc@4.7.3 arch=linux-ppc64
+           ^mpich@3.0.4%gcc@4.7.3 arch=linux-ppc64
 
 .. graphviz::
 
    digraph {
-       "mpileaks@2.3\n%gcc@4.7.3\n=linux-ppc64" -> "mpich@3.0.4\n%gcc@4.7.3\n=linux-ppc64"
-       "mpileaks@2.3\n%gcc@4.7.3\n=linux-ppc64" -> "callpath@1.0\n%gcc@4.7.3+debug\n=linux-ppc64" -> "mpich@3.0.4\n%gcc@4.7.3\n=linux-ppc64"
-       "callpath@1.0\n%gcc@4.7.3+debug\n=linux-ppc64" -> "dyninst@8.1.2\n%gcc@4.7.3\n=linux-ppc64"
-       "dyninst@8.1.2\n%gcc@4.7.3\n=linux-ppc64" -> "libdwarf@20130729\n%gcc@4.7.3\n=linux-ppc64" -> "libelf@0.8.11\n%gcc@4.7.3\n=linux-ppc64"
-       "dyninst@8.1.2\n%gcc@4.7.3\n=linux-ppc64" -> "libelf@0.8.11\n%gcc@4.7.3\n=linux-ppc64"
+       "mpileaks@2.3\n%gcc@4.7.3\n arch=linux-ppc64" -> "mpich@3.0.4\n%gcc@4.7.3\n arch=linux-ppc64"
+       "mpileaks@2.3\n%gcc@4.7.3\n arch=linux-ppc64" -> "callpath@1.0\n%gcc@4.7.3+debug\n arch=linux-ppc64" -> "mpich@3.0.4\n%gcc@4.7.3\n arch=linux-ppc64"
+       "callpath@1.0\n%gcc@4.7.3+debug\n arch=linux-ppc64" -> "dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-ppc64"
+       "dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-ppc64" -> "libdwarf@20130729\n%gcc@4.7.3\n arch=linux-ppc64" -> "libelf@0.8.11\n%gcc@4.7.3\n arch=linux-ppc64"
+       "dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-ppc64" -> "libelf@0.8.11\n%gcc@4.7.3\n arch=linux-ppc64"
    }
 
 Here, all versions, compilers, and platforms are filled in, and there
@@ -1648,8 +1650,8 @@ point will Spack call the ``install()`` method for your package.
 Concretization in Spack is based on certain selection policies that
 tell Spack how to select, e.g., a version, when one is not specified
 explicitly.  Concretization policies are discussed in more detail in
-:ref:`site-configuration`.  Sites using Spack can customize them to
-match the preferences of their own users.
+:ref:`configuration`.  Sites using Spack can customize them to match
+the preferences of their own users.
 
 .. _spack-spec:
 
@@ -1666,9 +1668,9 @@ running ``spack spec``.  For example:
        ^libdwarf
            ^libelf
 
-   dyninst@8.0.1%gcc@4.7.3=linux-ppc64
-       ^libdwarf@20130729%gcc@4.7.3=linux-ppc64
-           ^libelf@0.8.13%gcc@4.7.3=linux-ppc64
+   dyninst@8.0.1%gcc@4.7.3 arch=linux-ppc64
+       ^libdwarf@20130729%gcc@4.7.3 arch=linux-ppc64
+           ^libelf@0.8.13%gcc@4.7.3 arch=linux-ppc64
 
 This is useful when you want to know exactly what Spack will do when
 you ask for a particular spec.
@@ -1682,60 +1684,8 @@ be concretized on their system.  For example, one user may prefer packages
 built with OpenMPI and the Intel compiler.  Another user may prefer
 packages be built with MVAPICH and GCC.
 
-Spack can be configured to prefer certain compilers, package
-versions, depends_on, and variants during concretization.
-The preferred configuration can be controlled via the
-``~/.spack/packages.yaml`` file for user configuations, or the
-``etc/spack/packages.yaml`` site configuration.
-
-
-Here's an example packages.yaml file that sets preferred packages:
-
-.. code-block:: sh
-
-    packages:
-      dyninst:
-        compiler: [gcc@4.9]
-        variants: +debug
-      gperftools:
-        version: [2.2, 2.4, 2.3]
-      all:
-        compiler: [gcc@4.4.7, gcc@4.6:, intel, clang, pgi]
-        providers:
-          mpi: [mvapich, mpich, openmpi]
-
-
-At a high level, this example is specifying how packages should be
-concretized.  The dyninst package should prefer using gcc 4.9 and
-be built with debug options.  The gperftools package should prefer version
-2.2 over 2.4.  Every package on the system should prefer mvapich for
-its MPI and gcc 4.4.7 (except for Dyninst, which overrides this by preferring gcc 4.9).
-These options are used to fill in implicit defaults.  Any of them can be overwritten
-on the command line if explicitly requested.
-
-Each packages.yaml file begins with the string ``packages:`` and
-package names are specified on the next level. The special string ``all``
-applies settings to each package. Underneath each package name is
-one or more components: ``compiler``, ``variants``, ``version``,
-or ``providers``.  Each component has an ordered list of spec
-``constraints``, with earlier entries in the list being preferred over
-later entries.
-
-Sometimes a package installation may have constraints that forbid
-the first concretization rule, in which case Spack will use the first
-legal concretization rule.  Going back to the example, if a user
-requests gperftools 2.3 or later, then Spack will install version 2.4
-as the 2.4 version of gperftools is preferred over 2.3.
-
-An explicit concretization rule in the preferred section will always
-take preference over unlisted concretizations.  In the above example,
-xlc isn't listed in the compiler list.  Every listed compiler from
-gcc to pgi will thus be preferred over the xlc compiler.
-
-The syntax for the ``provider`` section differs slightly from other
-concretization rules.  A provider lists a value that packages may
-``depend_on`` (e.g, mpi) and a list of rules for fulfilling that
-dependency.
+See the `documentation in the config section <concretization-preferences_>`_
+for more details.
 
 .. _install-method:
 
@@ -1960,6 +1910,12 @@ the command line.
     ``$rpath_flag`` can be overriden on a compiler specific basis in
     ``lib/spack/spack/compilers/$compiler.py``.
 
+The compiler wrappers also pass the compiler flags specified by the user from
+the command line (``cflags``, ``cxxflags``, ``fflags``, ``cppflags``, ``ldflags``,
+and/or ``ldlibs``). They do not override the canonical autotools flags with the
+same names (but in ALL-CAPS) that may be passed into the build by particularly
+challenging package scripts.
+
 Compiler flags
 ~~~~~~~~~~~~~~
 In rare circumstances such as compiling and running small unit tests, a package
@@ -2206,12 +2162,12 @@ example:
        def install(self, prefix):
            # Do default install
 
-       @when('=chaos_5_x86_64_ib')
+       @when('arch=chaos_5_x86_64_ib')
        def install(self, prefix):
            # This will be executed instead of the default install if
            # the package's sys_type() is chaos_5_x86_64_ib.
 
-       @when('=bgqos_0")
+       @when('arch=bgqos_0")
        def install(self, prefix):
            # This will be executed if the package's sys_type is bgqos_0
 
@@ -2801,11 +2757,11 @@ build it:
    $ spack stage libelf
    ==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.13.tar.gz
    ######################################################################## 100.0%
-   ==> Staging archive: /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3=linux-ppc64/libelf-0.8.13.tar.gz
-   ==> Created stage in /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3=linux-ppc64.
+   ==> Staging archive: /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-ppc64/libelf-0.8.13.tar.gz
+   ==> Created stage in /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-ppc64.
    $ spack cd libelf
    $ pwd
-   /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3=linux-ppc64/libelf-0.8.13
+   /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-ppc64/libelf-0.8.13
 
 ``spack cd`` here changed he current working directory to the
 directory containing the expanded ``libelf`` source code.  There are a
diff --git a/lib/spack/spack/cmd/find.py b/lib/spack/spack/cmd/find.py
index c2bba13dc8..9649bc7435 100644
--- a/lib/spack/spack/cmd/find.py
+++ b/lib/spack/spack/cmd/find.py
@@ -38,71 +38,59 @@ description = "Find installed spack packages"
 
 def setup_parser(subparser):
     format_group = subparser.add_mutually_exclusive_group()
-    format_group.add_argument('-s',
-                              '--short',
+    format_group.add_argument('-s', '--short',
                               action='store_const',
                               dest='mode',
                               const='short',
                               help='Show only specs (default)')
-    format_group.add_argument('-p',
-                              '--paths',
+    format_group.add_argument('-p', '--paths',
                               action='store_const',
                               dest='mode',
                               const='paths',
                               help='Show paths to package install directories')
     format_group.add_argument(
-        '-d',
-        '--deps',
+        '-d', '--deps',
         action='store_const',
         dest='mode',
         const='deps',
         help='Show full dependency DAG of installed packages')
 
-    subparser.add_argument('-l',
-                           '--long',
+    subparser.add_argument('-l', '--long',
                            action='store_true',
                            dest='long',
                            help='Show dependency hashes as well as versions.')
-    subparser.add_argument('-L',
-                           '--very-long',
+    subparser.add_argument('-L', '--very-long',
                            action='store_true',
                            dest='very_long',
                            help='Show dependency hashes as well as versions.')
-    subparser.add_argument('-f',
-                           '--show-flags',
+    subparser.add_argument('-f', '--show-flags',
                            action='store_true',
                            dest='show_flags',
                            help='Show spec compiler flags.')
 
     subparser.add_argument(
-        '-e',
-        '--explicit',
+        '-e', '--explicit',
         action='store_true',
         help='Show only specs that were installed explicitly')
     subparser.add_argument(
-        '-E',
-        '--implicit',
+        '-E', '--implicit',
         action='store_true',
         help='Show only specs that were installed as dependencies')
     subparser.add_argument(
-        '-u',
-        '--unknown',
+        '-u', '--unknown',
         action='store_true',
         dest='unknown',
         help='Show only specs Spack does not have a package for.')
     subparser.add_argument(
-        '-m',
-        '--missing',
+        '-m', '--missing',
         action='store_true',
         dest='missing',
         help='Show missing dependencies as well as installed specs.')
-    subparser.add_argument('-M',
-                           '--only-missing',
+    subparser.add_argument('-M', '--only-missing',
                            action='store_true',
                            dest='only_missing',
                            help='Show only missing dependencies.')
-    subparser.add_argument('-N',
-                           '--namespace',
+    subparser.add_argument('-N', '--namespace',
                            action='store_true',
                            help='Show fully qualified package names.')
 
@@ -188,7 +176,32 @@ def display_specs(specs, **kwargs):
                     print(hsh + spec.format(format_string, color=True) + '\n')
 
         else:
-            raise ValueError("Invalid mode for display_specs: %s. Must be one of (paths, deps, short)." % mode)  # NOQA: ignore=E501
+            raise ValueError(
+                "Invalid mode for display_specs: %s. Must be one of (paths,"
+                "deps, short)." % mode)  # NOQA: ignore=E501
+
+
+def query_arguments(args):
+    # Check arguments
+    if args.explicit and args.implicit:
+        tty.error('You can\'t pass -E and -e options simultaneously.')
+        raise SystemExit(1)
+
+    # Set up query arguments.
+    installed, known = True, any
+    if args.only_missing:
+        installed = False
+    elif args.missing:
+        installed = any
+    if args.unknown:
+        known = False
+    explicit = any
+    if args.explicit:
+        explicit = True
+    if args.implicit:
+        explicit = False
+    q_args = {'installed': installed, 'known': known, "explicit": explicit}
+    return q_args
 
 
 def find(parser, args):
@@ -205,22 +218,7 @@ def find(parser, args):
         if not query_specs:
             return
 
-    # Set up query arguments.
-    installed, known = True, any
-    if args.only_missing:
-        installed = False
-    elif args.missing:
-        installed = any
-    if args.unknown:
-        known = False
-
-    explicit = any
-    if args.explicit:
-        explicit = False
-    if args.implicit:
-        explicit = True
-
-    q_args = {'installed': installed, 'known': known, "explicit": explicit}
+    q_args = query_arguments(args)
 
     # Get all the specs the user asked for
     if not query_specs:
diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py
index f3967e6b72..e768ddf5fe 100644
--- a/lib/spack/spack/database.py
+++ b/lib/spack/spack/database.py
@@ -40,7 +40,6 @@ filesystem.
 
 """
 import os
-import time
 import socket
 
 import yaml
@@ -56,6 +55,7 @@ from spack.spec import Spec
 from spack.error import SpackError
 from spack.repository import UnknownPackageError
 
+
 # DB goes in this directory underneath the root
 _db_dirname = '.spack-db'
 
@@ -69,10 +69,12 @@ _db_lock_timeout = 60
 def _autospec(function):
     """Decorator that automatically converts the argument of a single-arg
        function to a Spec."""
+
     def converter(self, spec_like, *args, **kwargs):
         if not isinstance(spec_like, spack.spec.Spec):
             spec_like = spack.spec.Spec(spec_like)
         return function(self, spec_like, *args, **kwargs)
+
     return converter
 
 
@@ -92,6 +94,7 @@ class InstallRecord(object):
     dependents left.
 
     """
+
     def __init__(self, spec, path, installed, ref_count=0, explicit=False):
         self.spec = spec
         self.path = str(path)
@@ -100,16 +103,19 @@ class InstallRecord(object):
         self.explicit = explicit
 
     def to_dict(self):
-        return { 'spec'      : self.spec.to_node_dict(),
-                 'path'      : self.path,
-                 'installed' : self.installed,
-                 'ref_count' : self.ref_count,
-                 'explicit'  : self.explicit }
+        return {
+            'spec': self.spec.to_node_dict(),
+            'path': self.path,
+            'installed': self.installed,
+            'ref_count': self.ref_count,
+            'explicit': self.explicit
+        }
 
     @classmethod
     def from_dict(cls, spec, dictionary):
         d = dictionary
-        return InstallRecord(spec, d['path'], d['installed'], d['ref_count'], d.get('explicit', False))
+        return InstallRecord(spec, d['path'], d['installed'], d['ref_count'],
+                             d.get('explicit', False))
 
 
 class Database(object):
@@ -144,7 +150,7 @@ class Database(object):
 
         # Set up layout of database files within the db dir
         self._index_path = join_path(self._db_dir, 'index.yaml')
-        self._lock_path  = join_path(self._db_dir, 'lock')
+        self._lock_path = join_path(self._db_dir, 'lock')
 
         # Create needed directories and files
         if not os.path.exists(self._db_dir):
@@ -157,17 +163,14 @@ class Database(object):
         self.lock = Lock(self._lock_path)
         self._data = {}
 
-
     def write_transaction(self, timeout=_db_lock_timeout):
         """Get a write lock context manager for use in a `with` block."""
         return WriteTransaction(self, self._read, self._write, timeout)
 
-
     def read_transaction(self, timeout=_db_lock_timeout):
         """Get a read lock context manager for use in a `with` block."""
         return ReadTransaction(self, self._read, None, timeout)
 
-
     def _write_to_yaml(self, stream):
         """Write out the databsae to a YAML file.
 
@@ -183,9 +186,9 @@ class Database(object):
         # different paths, it can't differentiate.
         # TODO: fix this before we support multiple install locations.
         database = {
-            'database' : {
-                'installs' : installs,
-                'version' : str(_db_version)
+            'database': {
+                'installs': installs,
+                'version': str(_db_version)
             }
         }
 
@@ -194,15 +197,11 @@ class Database(object):
         except YAMLError as e:
             raise SpackYAMLError("error writing YAML database:", str(e))
 
-
     def _read_spec_from_yaml(self, hash_key, installs, parent_key=None):
         """Recursively construct a spec from a hash in a YAML database.
 
         Does not do any locking.
         """
-        if hash_key not in installs:
-            parent = read_spec(installs[parent_key]['path'])
-
         spec_dict = installs[hash_key]['spec']
 
         # Install records don't include hash with spec, so we add it in here
@@ -224,7 +223,6 @@ class Database(object):
         spec._mark_concrete()
         return spec
 
-
     def _read_from_yaml(self, stream):
         """
         Fill database from YAML, do not maintain old data
@@ -246,15 +244,15 @@ class Database(object):
             return
 
         def check(cond, msg):
-            if not cond: raise CorruptDatabaseError(self._index_path, msg)
+            if not cond:
+                raise CorruptDatabaseError(self._index_path, msg)
 
         check('database' in yfile, "No 'database' attribute in YAML.")
 
         # High-level file checks
         db = yfile['database']
         check('installs' in db, "No 'installs' in YAML DB.")
-        check('version'  in db, "No 'version' in YAML DB.")
-
+        check('version' in db, "No 'version' in YAML DB.")
 
         installs = db['installs']
 
@@ -277,25 +275,25 @@ class Database(object):
                 # hashes are the same.
                 spec_hash = spec.dag_hash()
                 if not spec_hash == hash_key:
-                    tty.warn("Hash mismatch in database: %s -> spec with hash %s"
-                             % (hash_key, spec_hash))
-                    continue    # TODO: is skipping the right thing to do?
+                    tty.warn(
+                        "Hash mismatch in database: %s -> spec with hash %s" %
+                        (hash_key, spec_hash))
+                    continue  # TODO: is skipping the right thing to do?
 
                 # Insert the brand new spec in the database.  Each
                 # spec has its own copies of its dependency specs.
-                # TODO: would a more immmutable spec implementation simplify this?
+                # TODO: would a more immmutable spec implementation simplify
+                #       this?
                 data[hash_key] = InstallRecord.from_dict(spec, rec)
 
             except Exception as e:
                 tty.warn("Invalid database reecord:",
                          "file:  %s" % self._index_path,
-                         "hash:  %s" % hash_key,
-                         "cause: %s" % str(e))
+                         "hash:  %s" % hash_key, "cause: %s" % str(e))
                 raise
 
         self._data = data
 
-
     def reindex(self, directory_layout):
         """Build database index from scratch based from a directory layout.
 
@@ -320,7 +318,6 @@ class Database(object):
                 self._data = old_data
                 raise
 
-
     def _check_ref_counts(self):
         """Ensure consistency of reference counts in the DB.
 
@@ -342,9 +339,8 @@ class Database(object):
             found = rec.ref_count
             if not expected == found:
                 raise AssertionError(
-                    "Invalid ref_count: %s: %d (expected %d), in DB %s"
-                    % (key, found, expected, self._index_path))
-
+                    "Invalid ref_count: %s: %d (expected %d), in DB %s" %
+                    (key, found, expected, self._index_path))
 
     def _write(self):
         """Write the in-memory database index to its file path.
@@ -366,7 +362,6 @@ class Database(object):
                 os.remove(temp_file)
             raise
 
-
     def _read(self):
         """Re-read Database from the data in the set location.
 
@@ -381,7 +376,6 @@ class Database(object):
             # reindex() takes its own write lock, so no lock here.
             self.reindex(spack.install_layout)
 
-
     def _add(self, spec, path, directory_layout=None, explicit=False):
         """Add an install record for spec at path to the database.
 
@@ -404,11 +398,11 @@ class Database(object):
             rec.path = path
 
         else:
-            self._data[key] = InstallRecord(spec, path, True, explicit=explicit)
+            self._data[key] = InstallRecord(spec, path, True,
+                                            explicit=explicit)
             for dep in spec.dependencies.values():
                 self._increment_ref_count(dep, directory_layout)
 
-
     def _increment_ref_count(self, spec, directory_layout=None):
         """Recursively examine dependencies and update their DB entries."""
         key = spec.dag_hash()
@@ -438,28 +432,25 @@ class Database(object):
         with self.write_transaction():
             self._add(spec, path, explicit=explicit)
 
-
     def _get_matching_spec_key(self, spec, **kwargs):
         """Get the exact spec OR get a single spec that matches."""
         key = spec.dag_hash()
-        if not key in self._data:
+        if key not in self._data:
             match = self.query_one(spec, **kwargs)
             if match:
                 return match.dag_hash()
             raise KeyError("No such spec in database! %s" % spec)
         return key
 
-
     @_autospec
     def get_record(self, spec, **kwargs):
         key = self._get_matching_spec_key(spec, **kwargs)
         return self._data[key]
 
-
     def _decrement_ref_count(self, spec):
         key = spec.dag_hash()
 
-        if not key in self._data:
+        if key not in self._data:
             # TODO: print something here?  DB is corrupt, but
             # not much we can do.
             return
@@ -472,7 +463,6 @@ class Database(object):
             for dep in spec.dependencies.values():
                 self._decrement_ref_count(dep)
 
-
     def _remove(self, spec):
         """Non-locking version of remove(); does real work.
         """
@@ -491,7 +481,6 @@ class Database(object):
         # query spec was passed in.
         return rec.spec
 
-
     @_autospec
     def remove(self, spec):
         """Removes a spec from the database.  To be called on uninstall.
@@ -508,7 +497,6 @@ class Database(object):
         with self.write_transaction():
             return self._remove(spec)
 
-
     @_autospec
     def installed_extensions_for(self, extendee_spec):
         """
@@ -519,12 +507,11 @@ class Database(object):
             try:
                 if s.package.extends(extendee_spec):
                     yield s.package
-            except UnknownPackageError as e:
+            except UnknownPackageError:
                 continue
             # skips unknown packages
             # TODO: conditional way to do this instead of catching exceptions
 
-
     def query(self, query_spec=any, known=any, installed=True, explicit=any):
         """Run a query on the database.
 
@@ -567,14 +554,14 @@ class Database(object):
                     continue
                 if explicit is not any and rec.explicit != explicit:
                     continue
-                if known is not any and spack.repo.exists(rec.spec.name) != known:
+                if known is not any and spack.repo.exists(
+                        rec.spec.name) != known:
                     continue
                 if query_spec is any or rec.spec.satisfies(query_spec):
                     results.append(rec.spec)
 
             return sorted(results)
 
-
     def query_one(self, query_spec, known=any, installed=True):
         """Query for exactly one spec that matches the query spec.
 
@@ -586,10 +573,9 @@ class Database(object):
         assert len(concrete_specs) <= 1
         return concrete_specs[0] if concrete_specs else None
 
-
     def missing(self, spec):
         with self.read_transaction():
-            key =  spec.dag_hash()
+            key = spec.dag_hash()
             return key in self._data and not self._data[key].installed
 
 
@@ -601,7 +587,10 @@ class _Transaction(object):
 
     Timeout for lock is customizable.
     """
-    def __init__(self, db, acquire_fn=None, release_fn=None,
+
+    def __init__(self, db,
+                 acquire_fn=None,
+                 release_fn=None,
                  timeout=_db_lock_timeout):
         self._db = db
         self._timeout = timeout
@@ -636,11 +625,11 @@ class WriteTransaction(_Transaction):
 class CorruptDatabaseError(SpackError):
     def __init__(self, path, msg=''):
         super(CorruptDatabaseError, self).__init__(
-            "Spack database is corrupt: %s.  %s" %(path, msg))
+            "Spack database is corrupt: %s.  %s" % (path, msg))
 
 
 class InvalidDatabaseVersionError(SpackError):
     def __init__(self, expected, found):
         super(InvalidDatabaseVersionError, self).__init__(
-            "Expected database version %s but found version %s"
-            % (expected, found))
+            "Expected database version %s but found version %s" %
+            (expected, found))
diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index 7c8cebe0c9..1953d7c1b3 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -1,4 +1,4 @@
-##############################################################################
+#
 # Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
@@ -21,7 +21,7 @@
 # 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
-##############################################################################
+#
 """
 Fetch strategies are used to download source code into a staging area
 in order to build it.  They need to define the following methods:
@@ -75,11 +75,13 @@ def _needs_stage(fun):
 
 
 class FetchStrategy(object):
+
     """Superclass of all fetch strategies."""
     enabled = False  # Non-abstract subclasses should be enabled.
     required_attributes = None  # Attributes required in version() args.
 
     class __metaclass__(type):
+
         """This metaclass registers all fetch strategies in a list."""
 
         def __init__(cls, name, bases, dict):
@@ -126,6 +128,7 @@ class FetchStrategy(object):
 
 @pattern.composite(interface=FetchStrategy)
 class FetchStrategyComposite(object):
+
     """
     Composite for a FetchStrategy object. Implements the GoF composite pattern.
     """
@@ -134,6 +137,7 @@ class FetchStrategyComposite(object):
 
 
 class URLFetchStrategy(FetchStrategy):
+
     """FetchStrategy that pulls source code from a URL for an archive,
        checks the archive against a checksum,and decompresses the archive.
     """
@@ -235,12 +239,13 @@ class URLFetchStrategy(FetchStrategy):
         # redirects properly.
         content_types = re.findall(r'Content-Type:[^\r\n]+', headers)
         if content_types and 'text/html' in content_types[-1]:
-            tty.warn(
-                "The contents of " + self.archive_file + " look like HTML.",
-                "The checksum will likely be bad.  If it is, you can use",
-                "'spack clean <package>' to remove the bad archive, then fix",
-                "your internet gateway issue and install again.")
-
+            tty.warn("The contents of ",
+                     (self.archive_file if self.archive_file is not None
+                      else "the archive"),
+                     " look like HTML.",
+                     "The checksum will likely be bad.  If it is, you can use",
+                     "'spack clean <package>' to remove the bad archive, then",
+                     "fix your internet gateway issue and install again.")
         if save_file:
             os.rename(partial_file, save_file)
 
@@ -353,6 +358,7 @@ class URLFetchStrategy(FetchStrategy):
 
 
 class VCSFetchStrategy(FetchStrategy):
+
     def __init__(self, name, *rev_types, **kwargs):
         super(VCSFetchStrategy, self).__init__()
         self.name = name
@@ -407,6 +413,7 @@ class VCSFetchStrategy(FetchStrategy):
 
 
 class GoFetchStrategy(VCSFetchStrategy):
+
     """
     Fetch strategy that employs the `go get` infrastructure
     Use like this in a package:
@@ -466,6 +473,7 @@ class GoFetchStrategy(VCSFetchStrategy):
 
 
 class GitFetchStrategy(VCSFetchStrategy):
+
     """
     Fetch strategy that gets source code from a git repository.
     Use like this in a package:
@@ -586,6 +594,7 @@ class GitFetchStrategy(VCSFetchStrategy):
 
 
 class SvnFetchStrategy(VCSFetchStrategy):
+
     """Fetch strategy that gets source code from a subversion repository.
        Use like this in a package:
 
@@ -662,6 +671,7 @@ class SvnFetchStrategy(VCSFetchStrategy):
 
 
 class HgFetchStrategy(VCSFetchStrategy):
+
     """
     Fetch strategy that gets source code from a Mercurial repository.
     Use like this in a package:
@@ -806,11 +816,13 @@ def for_package_version(pkg, version):
 
 
 class FetchError(spack.error.SpackError):
+
     def __init__(self, msg, long_msg=None):
         super(FetchError, self).__init__(msg, long_msg)
 
 
 class FailedDownloadError(FetchError):
+
     """Raised wen a download fails."""
 
     def __init__(self, url, msg=""):
@@ -820,16 +832,19 @@ class FailedDownloadError(FetchError):
 
 
 class NoArchiveFileError(FetchError):
+
     def __init__(self, msg, long_msg):
         super(NoArchiveFileError, self).__init__(msg, long_msg)
 
 
 class NoDigestError(FetchError):
+
     def __init__(self, msg, long_msg=None):
         super(NoDigestError, self).__init__(msg, long_msg)
 
 
 class InvalidArgsError(FetchError):
+
     def __init__(self, pkg, version):
         msg = ("Could not construct a fetch strategy for package %s at "
                "version %s")
@@ -838,6 +853,7 @@ class InvalidArgsError(FetchError):
 
 
 class ChecksumError(FetchError):
+
     """Raised when archive fails to checksum."""
 
     def __init__(self, message, long_msg=None):
@@ -845,6 +861,7 @@ class ChecksumError(FetchError):
 
 
 class NoStageError(FetchError):
+
     """Raised when fetch operations are called before set_stage()."""
 
     def __init__(self, method):
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index bbc1abfa9e..a505b3c12e 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -129,24 +129,24 @@ from spack.build_environment import get_path_from_module, load_module
 identifier_re = r'\w[\w-]*'
 
 # Convenient names for color formats so that other things can use them
-compiler_color         = '@g'
-version_color          = '@c'
-architecture_color     = '@m'
-enabled_variant_color  = '@B'
+compiler_color = '@g'
+version_color = '@c'
+architecture_color = '@m'
+enabled_variant_color = '@B'
 disabled_variant_color = '@r'
-dependency_color       = '@.'
-hash_color             = '@K'
+dependency_color = '@.'
+hash_color = '@K'
 
 """This map determines the coloring of specs when using color output.
    We make the fields different colors to enhance readability.
    See spack.color for descriptions of the color codes. """
-color_formats = {'%' : compiler_color,
-                 '@' : version_color,
-                 '=' : architecture_color,
-                 '+' : enabled_variant_color,
-                 '~' : disabled_variant_color,
-                 '^' : dependency_color,
-                 '#' : hash_color }
+color_formats = {'%': compiler_color,
+                 '@': version_color,
+                 '=': architecture_color,
+                 '+': enabled_variant_color,
+                 '~': disabled_variant_color,
+                 '^': dependency_color,
+                 '#': hash_color}
 
 """Regex used for splitting by spec field separators."""
 _separators = '[%s]' % ''.join(color_formats.keys())
@@ -155,6 +155,7 @@ _separators = '[%s]' % ''.join(color_formats.keys())
    every time we call str()"""
 _any_version = VersionList([':'])
 
+
 def index_specs(specs):
     """Take a list of specs and return a dict of lists.  Dict is
        keyed by spec name and lists include all specs with the
@@ -162,7 +163,7 @@ def index_specs(specs):
     """
     spec_dict = {}
     for spec in specs:
-        if not spec.name in spec_dict:
+        if spec.name not in spec_dict:
             spec_dict[spec.name] = []
         spec_dict[spec.name].append(spec)
     return spec_dict
@@ -209,8 +210,8 @@ class CompilerSpec(object):
 
             else:
                 raise TypeError(
-                    "Can only build CompilerSpec from string or CompilerSpec." +
-                    "  Found %s" % type(arg))
+                    "Can only build CompilerSpec from string or " +
+                    "CompilerSpec. Found %s" % type(arg))
 
         elif nargs == 2:
             name, version = args
@@ -222,23 +223,19 @@ class CompilerSpec(object):
             raise TypeError(
                 "__init__ takes 1 or 2 arguments. (%d given)" % nargs)
 
-
     def _add_version(self, version):
         self.versions.add(version)
 
-
     def _autospec(self, compiler_spec_like):
         if isinstance(compiler_spec_like, CompilerSpec):
             return compiler_spec_like
         return CompilerSpec(compiler_spec_like)
 
-
     def satisfies(self, other, strict=False):
         other = self._autospec(other)
         return (self.name == other.name and
                 self.versions.satisfies(other.versions, strict=strict))
 
-
     def constrain(self, other):
         """Intersect self's versions with other.
 
@@ -252,44 +249,37 @@ class CompilerSpec(object):
 
         return self.versions.intersect(other.versions)
 
-
     @property
     def concrete(self):
         """A CompilerSpec is concrete if its versions are concrete and there
            is an available compiler with the right version."""
         return self.versions.concrete
 
-
     @property
     def version(self):
         if not self.concrete:
             raise SpecError("Spec is not concrete: " + str(self))
         return self.versions[0]
 
-
     def copy(self):
         clone = CompilerSpec.__new__(CompilerSpec)
         clone.name = self.name
         clone.versions = self.versions.copy()
         return clone
 
-
     def _cmp_key(self):
         return (self.name, self.versions)
 
-
     def to_dict(self):
-        d = {'name' : self.name}
+        d = {'name': self.name}
         d.update(self.versions.to_dict())
-        return { 'compiler' : d }
-
+        return {'compiler': d}
 
     @staticmethod
     def from_dict(d):
         d = d['compiler']
         return CompilerSpec(d['name'], VersionList.from_dict(d))
 
-
     def __str__(self):
         out = self.name
         if self.versions and self.versions != _any_version:
@@ -303,6 +293,7 @@ class CompilerSpec(object):
 
 @key_ordering
 class VariantSpec(object):
+
     """Variants are named, build-time options for a package.  Names depend
        on the particular package being built, and each named variant can
        be enabled or disabled.
@@ -311,17 +302,14 @@ class VariantSpec(object):
         self.name = name
         self.value = value
 
-
     def _cmp_key(self):
         return (self.name, self.value)
 
-
     def copy(self):
         return VariantSpec(self.name, self.value)
 
-
     def __str__(self):
-        if self.value in [True,False]:
+        if self.value in [True, False]:
             out = '+' if self.value else '~'
             return out + self.name
         else:
@@ -329,11 +317,11 @@ class VariantSpec(object):
 
 
 class VariantMap(HashableMap):
+
     def __init__(self, spec):
         super(VariantMap, self).__init__()
         self.spec = spec
 
-
     def satisfies(self, other, strict=False):
         if strict or self.spec._concrete:
             return all(k in self and self[k].value == other[k].value
@@ -342,7 +330,6 @@ class VariantMap(HashableMap):
             return all(self[k].value == other[k].value
                        for k in other if k in self)
 
-
     def constrain(self, other):
         """Add all variants in other that aren't in self to self.
 
@@ -361,7 +348,7 @@ class VariantMap(HashableMap):
                     raise UnsatisfiableVariantSpecError(self[k], other[k])
             else:
                 self[k] = other[k].copy()
-                changed =True
+                changed = True
         return changed
 
     @property
@@ -369,14 +356,12 @@ class VariantMap(HashableMap):
         return self.spec._concrete or all(
             v in self for v in self.spec.package_class.variants)
 
-
     def copy(self):
         clone = VariantMap(None)
         for name, variant in self.items():
             clone[name] = variant.copy()
         return clone
 
-
     def __str__(self):
         sorted_keys = sorted(self.keys())
         return ''.join(str(self[key]) for key in sorted_keys)
@@ -385,20 +370,20 @@ class VariantMap(HashableMap):
 _valid_compiler_flags = [
     'cflags', 'cxxflags', 'fflags', 'ldflags', 'ldlibs', 'cppflags']
 
+
 class FlagMap(HashableMap):
+
     def __init__(self, spec):
         super(FlagMap, self).__init__()
         self.spec = spec
 
-
     def satisfies(self, other, strict=False):
         if strict or (self.spec and self.spec._concrete):
             return all(f in self and set(self[f]) <= set(other[f])
                        for f in other)
         else:
             return all(set(self[f]) <= set(other[f])
-                   for f in other if (other[f] != [] and f in self))
-
+                       for f in other if (other[f] != [] and f in self))
 
     def constrain(self, other):
         """Add all flags in other that aren't in self to self.
@@ -408,13 +393,15 @@ class FlagMap(HashableMap):
         if other.spec and other.spec._concrete:
             for k in self:
                 if k not in other:
-                    raise UnsatisfiableCompilerFlagSpecError(self[k], '<absent>')
+                    raise UnsatisfiableCompilerFlagSpecError(
+                        self[k], '<absent>')
 
         changed = False
         for k in other:
             if k in self and not set(self[k]) <= set(other[k]):
                 raise UnsatisfiableCompilerFlagSpecError(
-                    ' '.join(f for f in self[k]), ' '.join( f for f in other[k]))
+                    ' '.join(f for f in self[k]),
+                    ' '.join(f for f in other[k]))
             elif k not in self:
                 self[k] = other[k]
                 changed = True
@@ -428,32 +415,33 @@ class FlagMap(HashableMap):
     def concrete(self):
         return all(flag in self for flag in _valid_compiler_flags)
 
-
     def copy(self):
         clone = FlagMap(None)
         for name, value in self.items():
             clone[name] = value
         return clone
 
-
     def _cmp_key(self):
-        return ''.join(str(key) + ' '.join(str(v) for v in value) for key, value in sorted(self.items()))
-
+        return ''.join(str(key) + ' '.join(str(v) for v in value)
+                       for key, value in sorted(self.items()))
 
     def __str__(self):
-        sorted_keys = filter(lambda flag: self[flag] != [], sorted(self.keys()))
-        cond_symbol = ' ' if len(sorted_keys)>0 else ''
-        return cond_symbol + ' '.join(str(key) + '=\"' + ' '.join(str(f) for f in self[key]) + '\"' for key in sorted_keys)
+        sorted_keys = filter(
+            lambda flag: self[flag] != [], sorted(self.keys()))
+        cond_symbol = ' ' if len(sorted_keys) > 0 else ''
+        return cond_symbol + ' '.join(str(key) + '=\"' + ' '.join(str(f)
+                                      for f in self[key]) + '\"'
+                                      for key in sorted_keys)
 
 
 class DependencyMap(HashableMap):
+
     """Each spec has a DependencyMap containing specs for its dependencies.
        The DependencyMap is keyed by name. """
     @property
     def concrete(self):
         return all(d.concrete for d in self.values())
 
-
     def __str__(self):
         return ''.join(
             ["^" + str(self[name]) for name in sorted(self.keys())])
@@ -461,6 +449,7 @@ class DependencyMap(HashableMap):
 
 @key_ordering
 class Spec(object):
+
     def __init__(self, spec_like, *dep_like, **kwargs):
         # Copy if spec_like is a Spec.
         if isinstance(spec_like, Spec):
@@ -513,7 +502,6 @@ class Spec(object):
             spec = dep if isinstance(dep, Spec) else Spec(dep)
             self._add_dependency(spec)
 
-
     #
     # Private routines here are called by the parser when building a spec.
     #
@@ -521,10 +509,10 @@ class Spec(object):
         """Called by the parser to add an allowable version."""
         self.versions.add(version)
 
-
     def _add_variant(self, name, value):
         """Called by the parser to add a variant."""
-        if name in self.variants: raise DuplicateVariantError(
+        if name in self.variants:
+            raise DuplicateVariantError(
                 "Cannot specify variant '%s' twice" % name)
         if isinstance(value, basestring) and value.upper() == 'TRUE':
             value = True
@@ -532,7 +520,6 @@ class Spec(object):
             value = False
         self.variants[name] = VariantSpec(name, value)
 
-
     def _add_flag(self, name, value):
         """Called by the parser to add a known flag.
         Known flags currently include "arch"
@@ -564,11 +551,12 @@ class Spec(object):
             assert(self.compiler_flags is not None)
             self.compiler_flags[name] = value.split()
         else:
-            self._add_variant(name,value)
+            self._add_variant(name, value)
 
     def _set_compiler(self, compiler):
         """Called by the parser to set the compiler."""
-        if self.compiler: raise DuplicateCompilerSpecError(
+        if self.compiler:
+            raise DuplicateCompilerSpecError(
                 "Spec for '%s' cannot have two compilers." % self.name)
         self.compiler = compiler
 
@@ -617,7 +605,8 @@ class Spec(object):
     def _add_dependency(self, spec):
         """Called by the parser to add another spec as a dependency."""
         if spec.name in self.dependencies:
-            raise DuplicateDependencyError("Cannot depend on '%s' twice" % spec)
+            raise DuplicateDependencyError(
+                "Cannot depend on '%s' twice" % spec)
         self.dependencies[spec.name] = spec
         spec.dependents[self.name] = self
 
@@ -626,8 +615,8 @@ class Spec(object):
     #
     @property
     def fullname(self):
-        return '%s.%s' % (self.namespace, self.name) if self.namespace else (self.name if self.name else '')
-
+        return (('%s.%s' % (self.namespace, self.name)) if self.namespace else
+                           (self.name if self.name else ''))
 
     @property
     def root(self):
@@ -647,12 +636,10 @@ class Spec(object):
         assert(all(first_root is d.root for d in depiter))
         return first_root
 
-
     @property
     def package(self):
         return spack.repo.get(self)
 
-
     @property
     def package_class(self):
         """Internal package call gets only the class object for a package.
@@ -660,7 +647,6 @@ class Spec(object):
         """
         return spack.repo.get_pkg_class(self.name)
 
-
     @property
     def virtual(self):
         """Right now, a spec is virtual if no package exists with its name.
@@ -672,12 +658,10 @@ class Spec(object):
         """
         return Spec.is_virtual(self.name)
 
-
     @staticmethod
     def is_virtual(name):
         """Test if a name is virtual without requiring a Spec."""
-        return (not name is None) and ( not spack.repo.exists(name) )
-
+        return (name is not None) and (not spack.repo.exists(name))
 
     @property
     def concrete(self):
@@ -699,7 +683,6 @@ class Spec(object):
                               and self.dependencies.concrete)
         return self._concrete
 
-
     def traverse(self, visited=None, d=0, **kwargs):
         """Generic traversal of the DAG represented by this spec.
            This will yield each node in the spec.  Options:
@@ -743,14 +726,14 @@ class Spec(object):
 
         """
         # get initial values for kwargs
-        depth      = kwargs.get('depth', False)
-        key_fun    = kwargs.get('key', id)
+        depth = kwargs.get('depth', False)
+        key_fun = kwargs.get('key', id)
         if isinstance(key_fun, basestring):
             key_fun = attrgetter(key_fun)
         yield_root = kwargs.get('root', True)
-        cover      = kwargs.get('cover', 'nodes')
-        direction  = kwargs.get('direction', 'children')
-        order      = kwargs.get('order', 'pre')
+        cover = kwargs.get('cover', 'nodes')
+        direction = kwargs.get('direction', 'children')
+        order = kwargs.get('order', 'pre')
 
         # Make sure kwargs have legal values; raise ValueError if not.
         def validate(name, val, allowed_values):
@@ -787,33 +770,29 @@ class Spec(object):
             visited.add(key)
             for name in sorted(successors):
                 child = successors[name]
-                for elt in child.traverse(visited, d+1, **kwargs):
+                for elt in child.traverse(visited, d + 1, **kwargs):
                     yield elt
 
         # Postorder traversal yields after successors
         if yield_me and order == 'post':
             yield result
 
-
     @property
     def short_spec(self):
         """Returns a version of the spec with the dependencies hashed
            instead of completely enumerated."""
         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))
 
-
     def dag_hash(self, length=None):
         """
         Return a hash of the entire spec DAG, including connectivity.
@@ -830,8 +809,9 @@ class Spec(object):
             return b32_hash
 
     def to_node_dict(self):
-        params = dict( (name, v.value) for name, v in self.variants.items() )
-        params.update( dict( (name, value) for name, value in self.compiler_flags.items()) )
+        params = dict((name, v.value) for name, v in self.variants.items())
+        params.update(dict((name, value)
+                      for name, value in self.compiler_flags.items()))
         d = {
             'parameters' : params,
             'arch' : self.architecture,
@@ -857,8 +837,7 @@ class Spec(object):
             d['compiler'] = None
         d.update(self.versions.to_dict())
 
-        return { self.name : d }
-
+        return {self.name: d}
 
     def to_yaml(self, stream=None):
         node_list = []
@@ -866,10 +845,9 @@ class Spec(object):
             node = s.to_node_dict()
             node[s.name]['hash'] = s.dag_hash()
             node_list.append(node)
-        return yaml.dump({ 'spec' : node_list },
+        return yaml.dump({'spec': node_list},
                          stream=stream, default_flow_style=False)
 
-
     @staticmethod
     def from_node_dict(node):
         name = next(iter(node))
@@ -901,11 +879,11 @@ class Spec(object):
             for name in FlagMap.valid_compiler_flags():
                 spec.compiler_flags[name] = []
         else:
-            raise SpackRecordError("Did not find a valid format for variants in YAML file")
+            raise SpackRecordError(
+                "Did not find a valid format for variants in YAML file")
 
         return spec
 
-
     @staticmethod
     def from_yaml(stream):
         """Construct a spec from YAML.
@@ -938,15 +916,16 @@ class Spec(object):
                 deps[name].dependencies[dep_name] = deps[dep_name]
         return spec
 
-
     def _concretize_helper(self, presets=None, visited=None):
         """Recursive helper function for concretize().
            This concretizes everything bottom-up.  As things are
            concretized, they're added to the presets, and ancestors
            will prefer the settings of their children.
         """
-        if presets is None: presets = {}
-        if visited is None: visited = set()
+        if presets is None:
+            presets = {}
+        if visited is None:
+            visited = set()
 
         if self.name in visited:
             return False
@@ -967,7 +946,8 @@ class Spec(object):
                 changed |= any(
                     (spack.concretizer.concretize_architecture(self),
                      spack.concretizer.concretize_compiler(self),
-                     spack.concretizer.concretize_compiler_flags(self),#has to be concretized after compiler
+                     spack.concretizer.concretize_compiler_flags(
+                         self),  # has to be concretized after compiler
                      spack.concretizer.concretize_version(self),
                      spack.concretizer.concretize_variants(self)))
             presets[self.name] = self
@@ -975,7 +955,6 @@ class Spec(object):
         visited.add(self.name)
         return changed
 
-
     def _replace_with(self, concrete):
         """Replace this virtual spec with a concrete spec."""
         assert(self.virtual)
@@ -987,7 +966,6 @@ class Spec(object):
             if concrete.name not in dependent.dependencies:
                 dependent._add_dependency(concrete)
 
-
     def _replace_node(self, replacement):
         """Replace this spec with another.
 
@@ -1005,7 +983,6 @@ class Spec(object):
             del dep.dependents[self.name]
             del self.dependencies[dep.name]
 
-
     def _expand_virtual_packages(self):
         """Find virtual packages in this spec, replace them with providers,
            and normalize again to include the provider's (potentially virtual)
@@ -1038,12 +1015,14 @@ class Spec(object):
                         # TODO: may break if in-place on self but
                         # shouldn't happen if root is traversed first.
                         spec._replace_with(replacement)
-                        done=False
+                        done = False
                         break
 
                 if not replacement:
-                    # Get a list of possible replacements in order of preference.
-                    candidates = spack.concretizer.choose_virtual_or_external(spec)
+                    # Get a list of possible replacements in order of
+                    # preference.
+                    candidates = spack.concretizer.choose_virtual_or_external(
+                        spec)
 
                     # Try the replacements in order, skipping any that cause
                     # satisfiability problems.
@@ -1056,11 +1035,12 @@ class Spec(object):
                         copy[spec.name]._dup(replacement.copy(deps=False))
 
                         try:
-                            # If there are duplicate providers or duplicate provider
-                            # deps, consolidate them and merge constraints.
+                            # If there are duplicate providers or duplicate
+                            # provider deps, consolidate them and merge
+                            # constraints.
                             copy.normalize(force=True)
                             break
-                        except SpecError as e:
+                        except SpecError:
                             # On error, we'll try the next replacement.
                             continue
 
@@ -1085,7 +1065,6 @@ class Spec(object):
                     feq(replacement.external, spec.external) and 
                     feq(replacement.external_module, spec.external_module)):
                     continue
-
                 # Refine this spec to the candidate. This uses
                 # replace_with AND dup so that it can work in
                 # place. TODO: make this more efficient.
@@ -1096,12 +1075,11 @@ class Spec(object):
                     changed = True
 
                 self_index.update(spec)
-                done=False
+                done = False
                 break
 
         return changed
 
-
     def concretize(self):
         """A spec is concrete if it describes one build of a package uniquely.
            This will ensure that this spec is concrete.
@@ -1110,9 +1088,9 @@ class Spec(object):
            of a package, this will add constraints to make it concrete.
 
            Some rigorous validation and checks are also performed on the spec.
-           Concretizing ensures that it is self-consistent and that it's consistent
-           with requirements of its pacakges.  See flatten() and normalize() for
-           more details on this.
+           Concretizing ensures that it is self-consistent and that it's
+           consistent with requirements of its pacakges.  See flatten() and
+           normalize() for more details on this.
         """
         if not self.name:
             raise SpecError("Attempting to concretize anonymous spec")
@@ -1128,7 +1106,7 @@ class Spec(object):
                        self._expand_virtual_packages(),
                        self._concretize_helper())
             changed = any(changes)
-            force=True
+            force = True
 
         for s in self.traverse():
             # After concretizing, assign namespaces to anything left.
@@ -1154,7 +1132,6 @@ class Spec(object):
         # Mark everything in the spec as concrete, as well.
         self._mark_concrete()
 
-
     def _mark_concrete(self):
         """Mark this spec and its dependencies as concrete.
 
@@ -1165,7 +1142,6 @@ class Spec(object):
             s._normal = True
             s._concrete = True
 
-
     def concretized(self):
         """This is a non-destructive version of concretize().  First clones,
            then returns a concrete version of this package without modifying
@@ -1174,7 +1150,6 @@ class Spec(object):
         clone.concretize()
         return clone
 
-
     def flat_dependencies(self, **kwargs):
         """Return a DependencyMap containing all of this spec's
            dependencies with their constraints merged.
@@ -1213,7 +1188,6 @@ class Spec(object):
             # parser doesn't allow it. Spack must be broken!
             raise InconsistentSpecError("Invalid Spec DAG: %s" % e.message)
 
-
     def index(self):
         """Return DependencyMap that points to all the dependencies in this
            spec."""
@@ -1222,7 +1196,6 @@ class Spec(object):
             dm[spec.name] = spec
         return dm
 
-
     def flatten(self):
         """Pull all dependencies up to the root (this spec).
            Merge constraints for dependencies with the same name, and if they
@@ -1230,7 +1203,6 @@ class Spec(object):
         for dep in self.flat_dependencies(copy=False):
             self._add_dependency(dep)
 
-
     def _evaluate_dependency_conditions(self, name):
         """Evaluate all the conditions on a dependency with this name.
 
@@ -1251,12 +1223,11 @@ class Spec(object):
                 try:
                     dep.constrain(dep_spec)
                 except UnsatisfiableSpecError, e:
-                    e.message = ("Conflicting conditional dependencies on package "
-                                 "%s for spec %s" % (self.name, self))
+                    e.message = ("Conflicting conditional dependencies on"
+                                 "package %s for spec %s" % (self.name, self))
                     raise e
         return dep
 
-
     def _find_provider(self, vdep, provider_index):
         """Find provider for a virtual spec in the provider index.
            Raise an exception if there is a conflicting virtual
@@ -1268,7 +1239,8 @@ class Spec(object):
         # If there is a provider for the vpkg, then use that instead of
         # the virtual package.
         if providers:
-            # Remove duplicate providers that can concretize to the same result.
+            # Remove duplicate providers that can concretize to the same
+            # result.
             for provider in providers:
                 for spec in providers:
                     if spec is not provider and provider.satisfies(spec):
@@ -1287,11 +1259,10 @@ class Spec(object):
             elif required:
                 raise UnsatisfiableProviderSpecError(required[0], vdep)
 
-
     def _merge_dependency(self, dep, visited, spec_deps, provider_index):
         """Merge the dependency into this spec.
 
-        This is the core of the normalize() method.  There are a few basic steps:
+        This is the core of normalize().  There are some basic steps:
 
           * If dep is virtual, evaluate whether it corresponds to an
             existing concrete dependency, and merge if so.
@@ -1335,7 +1306,7 @@ class Spec(object):
             changed |= spec_deps[dep.name].constrain(dep)
 
         except UnsatisfiableSpecError, e:
-            e.message =  "Invalid spec: '%s'. "
+            e.message = "Invalid spec: '%s'. "
             e.message += "Package %s requires %s %s, but spec asked for %s"
             e.message %= (spec_deps[dep.name], dep.name, e.constraint_type,
                           e.required, e.provided)
@@ -1346,10 +1317,10 @@ class Spec(object):
         if dep.name not in self.dependencies:
             self._add_dependency(dependency)
 
-        changed |= dependency._normalize_helper(visited, spec_deps, provider_index)
+        changed |= dependency._normalize_helper(
+            visited, spec_deps, provider_index)
         return changed
 
-
     def _normalize_helper(self, visited, spec_deps, provider_index):
         """Recursive helper function for _normalize."""
         if self.name in visited:
@@ -1380,22 +1351,22 @@ class Spec(object):
 
         return any_change
 
-
     def normalize(self, force=False):
         """When specs are parsed, any dependencies specified are hanging off
            the root, and ONLY the ones that were explicitly provided are there.
            Normalization turns a partial flat spec into a DAG, where:
 
            1. Known dependencies of the root package are in the DAG.
-           2. Each node's dependencies dict only contains its known direct deps.
+           2. Each node's dependencies dict only contains its known direct
+              deps.
            3. There is only ONE unique spec for each package in the DAG.
 
               * This includes virtual packages.  If there a non-virtual
                 package that provides a virtual package that is in the spec,
                 then we replace the virtual package with the non-virtual one.
 
-           TODO: normalize should probably implement some form of cycle detection,
-           to ensure that the spec is actually a DAG.
+           TODO: normalize should probably implement some form of cycle
+           detection, to ensure that the spec is actually a DAG.
         """
         if not self.name:
             raise SpecError("Attempting to normalize anonymous spec")
@@ -1429,14 +1400,14 @@ class Spec(object):
         self._normal = True
         return any_change
 
-
     def normalized(self):
-        """Return a normalized copy of this spec without modifying this spec."""
+        """
+        Return a normalized copy of this spec without modifying this spec.
+        """
         clone = self.copy()
         clone.normalize()
         return clone
 
-
     def validate_names(self):
         """This checks that names of packages and compilers in this spec are real.
            If they're not, it will raise either UnknownPackageError or
@@ -1457,7 +1428,6 @@ class Spec(object):
                 if vname not in spec.package_class.variants:
                     raise UnknownVariantError(spec.name, vname)
 
-
     def constrain(self, other, deps=True):
         """Merge the constraints of other with self.
 
@@ -1465,19 +1435,22 @@ class Spec(object):
         """
         other = self._autospec(other)
 
-        if not (self.name == other.name or (not self.name) or (not other.name) ):
+        if not (self.name == other.name or
+                (not self.name) or
+                (not other.name)):
             raise UnsatisfiableSpecNameError(self.name, other.name)
 
-        if other.namespace is not None:
-            if self.namespace is not None and other.namespace != self.namespace:
-                raise UnsatisfiableSpecNameError(self.fullname, other.fullname)
+        if (other.namespace is not None and
+           self.namespace is not None and
+           other.namespace != self.namespace):
+            raise UnsatisfiableSpecNameError(self.fullname, other.fullname)
 
         if not self.versions.overlaps(other.versions):
             raise UnsatisfiableVersionSpecError(self.versions, other.versions)
 
         for v in other.variants:
             if (v in self.variants and
-                self.variants[v].value != other.variants[v].value):
+                    self.variants[v].value != other.variants[v].value):
                 raise UnsatisfiableVariantSpecError(self.variants[v],
                                                     other.variants[v])
 
@@ -1526,7 +1499,6 @@ class Spec(object):
 
         return changed
 
-
     def _constrain_dependencies(self, other):
         """Apply constraints of other spec's dependencies to this spec."""
         other = self._autospec(other)
@@ -1545,7 +1517,6 @@ class Spec(object):
         for name in self.common_dependencies(other):
             changed |= self[name].constrain(other[name], deps=False)
 
-
         # Update with additional constraints from other spec
         for name in other.dep_difference(self):
             self._add_dependency(other[name].copy())
@@ -1553,7 +1524,6 @@ class Spec(object):
 
         return changed
 
-
     def common_dependencies(self, other):
         """Return names of dependencies that self an other have in common."""
         common = set(
@@ -1562,14 +1532,12 @@ class Spec(object):
             s.name for s in other.traverse(root=False))
         return common
 
-
     def constrained(self, other, deps=True):
         """Return a constrained copy without modifying this spec."""
         clone = self.copy(deps=deps)
         clone.constrain(other, deps)
         return clone
 
-
     def dep_difference(self, other):
         """Returns dependencies in self that are not in other."""
         mine = set(s.name for s in self.traverse(root=False))
@@ -1577,11 +1545,11 @@ class Spec(object):
             s.name for s in other.traverse(root=False))
         return mine
 
-
     def _autospec(self, spec_like):
-        """Used to convert arguments to specs.  If spec_like is a spec, returns it.
-           If it's a string, tries to parse a string.  If that fails, tries to parse
-           a local spec from it (i.e. name is assumed to be self's name).
+        """
+        Used to convert arguments to specs.  If spec_like is a spec, returns
+        it.  If it's a string, tries to parse a string.  If that fails, tries
+        to parse a local spec from it (i.e. name is assumed to be self's name).
         """
         if isinstance(spec_like, spack.spec.Spec):
             return spec_like
@@ -1589,12 +1557,12 @@ class Spec(object):
         try:
             spec = spack.spec.Spec(spec_like)
             if not spec.name:
-                raise SpecError("anonymous package -- this will always be handled")
+                raise SpecError(
+                    "anonymous package -- this will always be handled")
             return spec
         except SpecError:
             return parse_anonymous_spec(spec_like, self.name)
 
-
     def satisfies(self, other, deps=True, strict=False):
         """Determine if this spec satisfies all constraints of another.
 
@@ -1610,7 +1578,7 @@ class Spec(object):
         """
         other = self._autospec(other)
 
-        # a concrete provider can satisfy a virtual dependency.
+        # A concrete provider can satisfy a virtual dependency.
         if not self.virtual and other.virtual:
             pkg = spack.repo.get(self.fullname)
             if pkg.provides(other.name):
@@ -1625,10 +1593,10 @@ class Spec(object):
             return False
 
         # namespaces either match, or other doesn't require one.
-        if other.namespace is not None:
-            if self.namespace is not None and self.namespace != other.namespace:
-                return False
-
+        if (other.namespace is not None and
+            self.namespace is not None and
+           self.namespace != other.namespace):
+            return False
         if self.versions and other.versions:
             if not self.versions.satisfies(other.versions, strict=strict):
                 return False
@@ -1650,9 +1618,6 @@ class Spec(object):
 
         # Architecture satisfaction is currently just string equality.
         # If not strict, None means unconstrained.
-
-
-        # TODO: Need to make sure that comparisons can be made via classes
         if self.architecture and other.architecture:
             if ((self.architecture.platform and other.architecture.platform and self.architecture.platform != other.architecture.platform) or 
                 (self.architecture.platform_os and other.architecture.platform_os and self.architecture.platform_os != other.architecture.platform_os) or
@@ -1664,21 +1629,24 @@ class Spec(object):
                          (other.architecture.target and not self.architecture.target)):
             return False
 
-        if not self.compiler_flags.satisfies(other.compiler_flags, strict=strict):
+        if not self.compiler_flags.satisfies(
+                other.compiler_flags,
+                strict=strict):
             return False
 
         # If we need to descend into dependencies, do it, otherwise we're done.
         if deps:
             deps_strict = strict
             if not (self.name and other.name):
-                deps_strict=True
+                deps_strict = True
             return self.satisfies_dependencies(other, strict=deps_strict)
         else:
             return True
 
-
     def satisfies_dependencies(self, other, strict=False):
-        """This checks constraints on common dependencies against each other."""
+        """
+        This checks constraints on common dependencies against each other.
+        """
         other = self._autospec(other)
 
         if strict:
@@ -1689,7 +1657,8 @@ class Spec(object):
                 return False
 
         elif not self.dependencies or not other.dependencies:
-            # if either spec doesn't restrict dependencies then both are compatible.
+            # if either spec doesn't restrict dependencies then both are
+            # compatible.
             return True
 
         # Handle first-order constraints directly
@@ -1705,11 +1674,12 @@ class Spec(object):
         if not self_index.satisfies(other_index):
             return False
 
-        # These two loops handle cases where there is an overly restrictive vpkg
-        # in one spec for a provider in the other (e.g., mpi@3: is not compatible
-        # with mpich2)
+        # These two loops handle cases where there is an overly restrictive
+        # vpkg in one spec for a provider in the other (e.g., mpi@3: is not
+        # compatible with mpich2)
         for spec in self.virtual_dependencies():
-            if spec.name in other_index and not other_index.providers_for(spec):
+            if (spec.name in other_index and
+               not other_index.providers_for(spec)):
                 return False
 
         for spec in other.virtual_dependencies():
@@ -1718,12 +1688,10 @@ class Spec(object):
 
         return True
 
-
     def virtual_dependencies(self):
         """Return list of any virtual deps in this spec."""
         return [spec for spec in self.traverse() if spec.virtual]
 
-
     def _dup(self, other, **kwargs):
         """Copy the spec other into self.  This is an overwriting
            copy.  It does not copy any dependents (parents), but by default
@@ -1781,7 +1749,6 @@ class Spec(object):
         self.external_module = other.external_module
         return changed
 
-
     def copy(self, **kwargs):
         """Return a copy of this spec.
            By default, returns a deep copy.  Supply dependencies=False
@@ -1791,14 +1758,12 @@ class Spec(object):
         clone._dup(self, **kwargs)
         return clone
 
-
     @property
     def version(self):
         if not self.versions.concrete:
             raise SpecError("Spec version is not concrete: " + str(self))
         return self.versions[0]
 
-
     def __getitem__(self, name):
         """Get a dependency from the spec by its name."""
         for spec in self.traverse():
@@ -1817,7 +1782,6 @@ class Spec(object):
 
         raise KeyError("No spec with name %s in %s" % (name, self))
 
-
     def __contains__(self, spec):
         """True if this spec satisfis the provided spec, or if any dependency
            does.  If the spec has no name, then we parse this one first.
@@ -1829,13 +1793,11 @@ class Spec(object):
 
         return False
 
-
     def sorted_deps(self):
         """Return a list of all dependencies sorted by name."""
         deps = self.flat_dependencies()
         return tuple(deps[name] for name in sorted(deps))
 
-
     def _eq_dag(self, other, vs, vo):
         """Recursive helper for eq_dag and ne_dag.  Does the actual DAG
            traversal."""
@@ -1848,18 +1810,22 @@ class Spec(object):
         if len(self.dependencies) != len(other.dependencies):
             return False
 
-        ssorted = [self.dependencies[name]  for name in sorted(self.dependencies)]
-        osorted = [other.dependencies[name] for name in sorted(other.dependencies)]
+        ssorted = [self.dependencies[name]
+                   for name in sorted(self.dependencies)]
+        osorted = [other.dependencies[name]
+                   for name in sorted(other.dependencies)]
 
         for s, o in zip(ssorted, osorted):
             visited_s = id(s) in vs
             visited_o = id(o) in vo
 
             # Check for duplicate or non-equal dependencies
-            if visited_s != visited_o: return False
+            if visited_s != visited_o:
+                return False
 
             # Skip visited nodes
-            if visited_s or visited_o: continue
+            if visited_s or visited_o:
+                continue
 
             # Recursive check for equality
             if not s._eq_dag(o, vs, vo):
@@ -1867,17 +1833,14 @@ class Spec(object):
 
         return True
 
-
     def eq_dag(self, other):
         """True if the full dependency DAGs of specs are equal"""
         return self._eq_dag(other, set(), set())
 
-
     def ne_dag(self, other):
         """True if the full dependency DAGs of specs are not equal"""
         return not self.eq_dag(other)
 
-
     def _cmp_node(self):
         """Comparison key for just *this node* and not its deps."""
         return (self.name,
@@ -1893,12 +1856,10 @@ class Spec(object):
         """Equality with another spec, not including dependencies."""
         return self._cmp_node() == other._cmp_node()
 
-
     def ne_node(self, other):
         """Inequality with another spec, not including dependencies."""
         return self._cmp_node() != other._cmp_node()
 
-
     def _cmp_key(self):
         """This returns a key for the spec *including* DAG structure.
 
@@ -1910,55 +1871,56 @@ class Spec(object):
             tuple(hash(self.dependencies[name])
                   for name in sorted(self.dependencies)),)
 
-
     def colorized(self):
         return colorize_spec(self)
 
-
     def format(self, format_string='$_$@$%@+$+$=', **kwargs):
-        """Prints out particular pieces of a spec, depending on what is
-           in the format string.  The format strings you can provide are::
-
-               $_   Package name
-               $.   Full package name (with namespace)
-               $@   Version with '@' prefix
-               $%   Compiler with '%' prefix
-               $%@  Compiler with '%' prefix & compiler version with '@' prefix
-               $%+  Compiler with '%' prefix & compiler flags prefixed by name
-               $%@+ Compiler, compiler version, and compiler flags with same prefixes as above
-               $+   Options
-               $=   Architecture prefixed by 'arch='
-               $#   7-char prefix of DAG hash with '-' prefix
-               $$   $
-
-               You can also use full-string versions, which leave off the prefixes:
-
-               ${PACKAGE}       Package name
-               ${VERSION}       Version
-               ${COMPILER}      Full compiler string
-               ${COMPILERNAME}  Compiler name
-               ${COMPILERVER}   Compiler version
-               ${COMPILERFLAGS} Compiler flags
-               ${OPTIONS}       Options
-               ${ARCHITECTURE}  Architecture
-               ${SHA1}          Dependencies 8-char sha1 prefix
-
-               ${SPACK_ROOT}    The spack root directory
-               ${SPACK_INSTALL} The default spack install directory, ${SPACK_PREFIX}/opt
-
-           Optionally you can provide a width, e.g. $20_ for a 20-wide name.
-           Like printf, you can provide '-' for left justification, e.g.
-           $-20_ for a left-justified name.
-
-           Anything else is copied verbatim into the output stream.
-
-           *Example:*  ``$_$@$+`` translates to the name, version, and options
-           of the package, but no dependencies, architecture, or compiler.
-
-           TODO: allow, e.g., $6# to customize short hash length
-           TODO: allow, e.g., $## for full hash.
-           """
-        color    = kwargs.get('color', False)
+        """
+        Prints out particular pieces of a spec, depending on what is
+        in the format string.  The format strings you can provide are::
+
+            $_   Package name
+            $.   Full package name (with namespace)
+            $@   Version with '@' prefix
+            $%   Compiler with '%' prefix
+            $%@  Compiler with '%' prefix & compiler version with '@' prefix
+            $%+  Compiler with '%' prefix & compiler flags prefixed by name
+            $%@+ Compiler, compiler version, and compiler flags with same
+                 prefixes as above
+            $+   Options
+            $=   Architecture prefixed by 'arch='
+            $#   7-char prefix of DAG hash with '-' prefix
+            $$   $
+
+            You can also use full-string versions, which elide the prefixes:
+
+            ${PACKAGE}       Package name
+            ${VERSION}       Version
+            ${COMPILER}      Full compiler string
+            ${COMPILERNAME}  Compiler name
+            ${COMPILERVER}   Compiler version
+            ${COMPILERFLAGS} Compiler flags
+            ${OPTIONS}       Options
+            ${ARCHITECTURE}  Architecture
+            ${SHA1}          Dependencies 8-char sha1 prefix
+
+            ${SPACK_ROOT}    The spack root directory
+            ${SPACK_INSTALL} The default spack install directory,
+                             ${SPACK_PREFIX}/opt
+
+        Optionally you can provide a width, e.g. $20_ for a 20-wide name.
+        Like printf, you can provide '-' for left justification, e.g.
+        $-20_ for a left-justified name.
+
+        Anything else is copied verbatim into the output stream.
+
+        *Example:*  ``$_$@$+`` translates to the name, version, and options
+        of the package, but no dependencies, arch, or compiler.
+
+        TODO: allow, e.g., $6# to customize short hash length
+        TODO: allow, e.g., $## for full hash.
+        """
+        color = kwargs.get('color', False)
         length = len(format_string)
         out = StringIO()
         named = escape = compiler = False
@@ -2016,7 +1978,7 @@ class Spec(object):
             elif compiler:
                 if c == '@':
                     if (self.compiler and self.compiler.versions and
-                        self.compiler.versions != _any_version):
+                            self.compiler.versions != _any_version):
                         write(c + str(self.compiler.versions), '%')
                 elif c == '+':
                     if self.compiler_flags:
@@ -2032,10 +1994,10 @@ class Spec(object):
             elif named:
                 if not c == '}':
                     if i == length - 1:
-                        raise ValueError("Error: unterminated ${ in format: '%s'"
-                                         % format_string)
+                        raise ValueError("Error: unterminated ${ in format:"
+                                         "'%s'" % format_string)
                     named_str += c
-                    continue;
+                    continue
                 if named_str == 'PACKAGE':
                     name = self.name if self.name else ''
                     write(fmt % self.name, '@')
@@ -2081,7 +2043,6 @@ class Spec(object):
         result = out.getvalue()
         return result
 
-
     def dep_string(self):
         return ''.join("^" + dep.format() for dep in self.sorted_deps())
 
@@ -2123,16 +2084,15 @@ class Spec(object):
     def __str__(self):
         return self.format() + self.dep_string()
 
-
     def tree(self, **kwargs):
         """Prints out this spec and its dependencies, tree-formatted
            with indentation."""
-        color  = kwargs.pop('color', False)
-        depth  = kwargs.pop('depth', False)
+        color = kwargs.pop('color', False)
+        depth = kwargs.pop('depth', False)
         showid = kwargs.pop('ids',   False)
-        cover  = kwargs.pop('cover', 'nodes')
+        cover = kwargs.pop('cover', 'nodes')
         indent = kwargs.pop('indent', 0)
-        fmt    = kwargs.pop('format', '$_$@$%@+$+$=')
+        fmt = kwargs.pop('format', '$_$@$%@+$+$=')
         prefix = kwargs.pop('prefix', None)
         check_kwargs(kwargs, self.tree)
 
@@ -2156,7 +2116,6 @@ class Spec(object):
             out += node.format(fmt, color=color) + "\n"
         return out
 
-
     def __repr__(self):
         return str(self)
 
@@ -2166,28 +2125,33 @@ class Spec(object):
 #
 HASH, DEP, AT, COLON, COMMA, ON, OFF, PCT, EQ, QT, ID = range(11)
 
+
 class SpecLexer(spack.parse.Lexer):
+
     """Parses tokens that make up spack specs."""
+
     def __init__(self):
         super(SpecLexer, self).__init__([
-            (r'/',         lambda scanner, val: self.token(HASH,  val)),
-            (r'\^',        lambda scanner, val: self.token(DEP,   val)),
-            (r'\@',        lambda scanner, val: self.token(AT,    val)),
-            (r'\:',        lambda scanner, val: self.token(COLON, val)),
-            (r'\,',        lambda scanner, val: self.token(COMMA, val)),
-            (r'\+',        lambda scanner, val: self.token(ON,    val)),
-            (r'\-',        lambda scanner, val: self.token(OFF,   val)),
-            (r'\~',        lambda scanner, val: self.token(OFF,   val)),
-            (r'\%',        lambda scanner, val: self.token(PCT,   val)),
-            (r'\=',        lambda scanner, val: self.token(EQ,    val)),
+            (r'/', lambda scanner, val: self.token(HASH,  val)),
+            (r'\^', lambda scanner, val: self.token(DEP,   val)),
+            (r'\@', lambda scanner, val: self.token(AT,    val)),
+            (r'\:', lambda scanner, val: self.token(COLON, val)),
+            (r'\,', lambda scanner, val: self.token(COMMA, val)),
+            (r'\+', lambda scanner, val: self.token(ON,    val)),
+            (r'\-', lambda scanner, val: self.token(OFF,   val)),
+            (r'\~', lambda scanner, val: self.token(OFF,   val)),
+            (r'\%', lambda scanner, val: self.token(PCT,   val)),
+            (r'\=', lambda scanner, val: self.token(EQ,    val)),
             # This is more liberal than identifier_re (see above).
             # Checked by check_identifier() for better error messages.
-            (r'([\"\'])(?:(?=(\\?))\2.)*?\1',lambda scanner, val: self.token(QT, val)),
+            (r'([\"\'])(?:(?=(\\?))\2.)*?\1',
+             lambda scanner, val: self.token(QT, val)),
             (r'\w[\w.-]*', lambda scanner, val: self.token(ID,    val)),
-            (r'\s+',       lambda scanner, val: None)])
+            (r'\s+', lambda scanner, val: None)])
 
 
 class SpecParser(spack.parse.Parser):
+
     def __init__(self):
         super(SpecParser, self).__init__(SpecLexer())
         self.previous = None
@@ -2208,7 +2172,8 @@ class SpecParser(spack.parse.Parser):
                             self.token.value = self.token.value[1:-1]
                         else:
                             self.expect(ID)
-                        specs[-1]._add_flag(self.previous.value, self.token.value)
+                        specs[-1]._add_flag(
+                            self.previous.value, self.token.value)
                     else:
                         specs.append(self.spec(self.previous.value))
                     self.previous = None
@@ -2227,9 +2192,11 @@ class SpecParser(spack.parse.Parser):
                         specs[-1]._add_dependency(self.spec(self.token.value))
 
                 else:
-                    # Attempt to construct an anonymous spec, but check that the first token is valid
-                    # TODO: Is this check even necessary, or will it all be Lex errors now?
-                    specs.append(self.spec(None,True))
+                    # Attempt to construct an anonymous spec, but check that
+                    # the first token is valid
+                    # TODO: Is this check even necessary, or will it all be Lex
+                    # errors now?
+                    specs.append(self.spec(None, True))
 
         except spack.parse.ParseError, e:
             raise SpecParseError(e)
@@ -2242,12 +2209,10 @@ class SpecParser(spack.parse.Parser):
                     s._set_platform(spack.architecture.sys_type())
         return specs
 
-
     def parse_compiler(self, text):
         self.setup(text)
         return self.compiler()
 
-
     def spec_by_hash(self):
         self.expect(ID)
 
@@ -2256,15 +2221,17 @@ class SpecParser(spack.parse.Parser):
                    spec.dag_hash()[:len(self.token.value)] == self.token.value]
 
         if not matches:
-            tty.die("%s does not match any installed packages." %self.token.value)
+            tty.die("%s does not match any installed packages." %
+                    self.token.value)
 
         if len(matches) != 1:
-            raise AmbiguousHashError("Multiple packages specify hash %s." % self.token.value, *matches)
+            raise AmbiguousHashError(
+                "Multiple packages specify hash %s." % self.token.value,
+                *matches)
 
         return matches[0]
 
-
-    def spec(self, name, check_valid_token = False):
+    def spec(self, name, check_valid_token=False):
         """Parse a spec out of the input.  If a spec is supplied, then initialize
            and return it instead of creating a new one."""
         if name:
@@ -2276,8 +2243,6 @@ class SpecParser(spack.parse.Parser):
             spec_namespace = None
             spec_name = None
 
-
-
         # This will init the spec without calling __init__.
         spec = Spec.__new__(Spec)
         spec.name = spec_name
@@ -2288,7 +2253,7 @@ class SpecParser(spack.parse.Parser):
         spec.external = None
         spec.external_module = None
         spec.compiler_flags = FlagMap(spec)
-        spec.dependents   = DependencyMap()
+        spec.dependents = DependencyMap()
         spec.dependencies = DependencyMap()
         spec.namespace = spec_namespace
         spec._hash = None
@@ -2306,7 +2271,8 @@ class SpecParser(spack.parse.Parser):
             else:
                 self.expect(ID)
                 if self.accept(EQ):
-                    raise SpecParseError(spack.parse.ParseError("","","Expected dependency received anonymous spec"))
+                    raise SpecParseError(spack.parse.ParseError(
+                        "", "", "Expected dependency received anonymous spec"))
                 spec.add_dependency(self.spec(self.token.value))
 
         while self.next:
@@ -2322,7 +2288,7 @@ class SpecParser(spack.parse.Parser):
                 check_valid_token = False
 
             elif self.accept(OFF):
-                spec._add_variant(self.variant(),False)
+                spec._add_variant(self.variant(), False)
                 check_valid_token = False
 
             elif self.accept(PCT):
@@ -2352,9 +2318,8 @@ class SpecParser(spack.parse.Parser):
 
         return spec
 
-
-    def variant(self,name=None):
-        #TODO: Make generalized variants possible
+    def variant(self, name=None):
+        # TODO: Make generalized variants possible
         if name:
             return name
         else:
@@ -2378,11 +2343,12 @@ class SpecParser(spack.parse.Parser):
             # No colon and no id: invalid version.
             self.next_token_error("Invalid version specifier")
 
-        if start: start = Version(start)
-        if end: end = Version(end)
+        if start:
+            start = Version(start)
+        if end:
+            end = Version(end)
         return VersionRange(start, end)
 
-
     def version_list(self):
         vlist = []
         vlist.append(self.version())
@@ -2390,7 +2356,6 @@ class SpecParser(spack.parse.Parser):
             vlist.append(self.version())
         return vlist
 
-
     def compiler(self):
         self.expect(ID)
         self.check_identifier()
@@ -2406,7 +2371,6 @@ class SpecParser(spack.parse.Parser):
             compiler.versions = VersionList(':')
         return compiler
 
-
     def check_identifier(self, id=None):
         """The only identifiers that can contain '.' are versions, but version
            ids are context-sensitive so we have to check on a case-by-case
@@ -2440,10 +2404,15 @@ def parse_anonymous_spec(spec_like, pkg_name):
         try:
             anon_spec = Spec(spec_like)
             if anon_spec.name != pkg_name:
-                raise SpecParseError(spack.parse.ParseError("","","Expected anonymous spec for package %s but found spec for package %s" % (pkg_name, anon_spec.name) ))
+                raise SpecParseError(spack.parse.ParseError(
+                    "",
+                    "",
+                    "Expected anonymous spec for package %s but found spec for"
+                    "package %s" % (pkg_name, anon_spec.name)))
         except SpecParseError:
-            anon_spec = Spec(pkg_name + ' ' +  spec_like)
-            if anon_spec.name != pkg_name: raise ValueError(
+            anon_spec = Spec(pkg_name + ' ' + spec_like)
+            if anon_spec.name != pkg_name:
+                raise ValueError(
                     "Invalid spec for package %s: %s" % (pkg_name, spec_like))
     else:
         anon_spec = spec_like.copy()
@@ -2456,12 +2425,17 @@ def parse_anonymous_spec(spec_like, pkg_name):
 
 
 class SpecError(spack.error.SpackError):
+
     """Superclass for all errors that occur while constructing specs."""
+
     def __init__(self, message):
         super(SpecError, self).__init__(message)
 
+
 class SpecParseError(SpecError):
+
     """Wrapper for ParseError for when we're parsing specs."""
+
     def __init__(self, parse_error):
         super(SpecParseError, self).__init__(parse_error.message)
         self.string = parse_error.string
@@ -2469,68 +2443,79 @@ class SpecParseError(SpecError):
 
 
 class DuplicateDependencyError(SpecError):
+
     """Raised when the same dependency occurs in a spec twice."""
+
     def __init__(self, message):
         super(DuplicateDependencyError, self).__init__(message)
 
 
 class DuplicateVariantError(SpecError):
+
     """Raised when the same variant occurs in a spec twice."""
+
     def __init__(self, message):
         super(DuplicateVariantError, self).__init__(message)
 
 
 class DuplicateCompilerSpecError(SpecError):
+
     """Raised when the same compiler occurs in a spec twice."""
+
     def __init__(self, message):
         super(DuplicateCompilerSpecError, self).__init__(message)
 
 
 class UnsupportedCompilerError(SpecError):
+
     """Raised when the user asks for a compiler spack doesn't know about."""
+
     def __init__(self, compiler_name):
         super(UnsupportedCompilerError, self).__init__(
             "The '%s' compiler is not yet supported." % compiler_name)
 
 
 class UnknownVariantError(SpecError):
+
     """Raised when the same variant occurs in a spec twice."""
+
     def __init__(self, pkg, variant):
         super(UnknownVariantError, self).__init__(
             "Package %s has no variant %s!" % (pkg, variant))
 
-class UnknownArchitectureSpecError(SpecError):
-    """ Raised when an entry in a string field is neither a platform,
-        operating system or a target. """
-    def __init__(self, architecture_spec_entry):
-        super(UnknownArchitectureSpecError, self).__init__(
-                "Architecture spec %s is not a valid spec entry" % (
-                                            architecture_spec_entry))
 
 class DuplicateArchitectureError(SpecError):
+
     """Raised when the same architecture occurs in a spec twice."""
+
     def __init__(self, message):
         super(DuplicateArchitectureError, self).__init__(message)
 
 
 class InconsistentSpecError(SpecError):
+
     """Raised when two nodes in the same spec DAG have inconsistent
        constraints."""
+
     def __init__(self, message):
         super(InconsistentSpecError, self).__init__(message)
 
 
 class InvalidDependencyException(SpecError):
+
     """Raised when a dependency in a spec is not actually a dependency
        of the package."""
+
     def __init__(self, message):
         super(InvalidDependencyException, self).__init__(message)
 
 
 class NoProviderError(SpecError):
+
     """Raised when there is no package that provides a particular
        virtual dependency.
     """
+
     def __init__(self, vpkg):
         super(NoProviderError, self).__init__(
             "No providers found for virtual package: '%s'" % vpkg)
@@ -2538,9 +2523,11 @@ class NoProviderError(SpecError):
 
 
 class MultipleProviderError(SpecError):
+
     """Raised when there is no package that provides a particular
        virtual dependency.
     """
+
     def __init__(self, vpkg, providers):
         """Takes the name of the vpkg"""
         super(MultipleProviderError, self).__init__(
@@ -2549,9 +2536,12 @@ class MultipleProviderError(SpecError):
         self.vpkg = vpkg
         self.providers = providers
 
+
 class UnsatisfiableSpecError(SpecError):
+
     """Raised when a spec conflicts with package constraints.
        Provide the requirement that was violated when raising."""
+
     def __init__(self, provided, required, constraint_type):
         super(UnsatisfiableSpecError, self).__init__(
             "%s does not satisfy %s" % (provided, required))
@@ -2561,69 +2551,95 @@ class UnsatisfiableSpecError(SpecError):
 
 
 class UnsatisfiableSpecNameError(UnsatisfiableSpecError):
+
     """Raised when two specs aren't even for the same package."""
+
     def __init__(self, provided, required):
         super(UnsatisfiableSpecNameError, self).__init__(
             provided, required, "name")
 
 
 class UnsatisfiableVersionSpecError(UnsatisfiableSpecError):
+
     """Raised when a spec version conflicts with package constraints."""
+
     def __init__(self, provided, required):
         super(UnsatisfiableVersionSpecError, self).__init__(
             provided, required, "version")
 
 
 class UnsatisfiableCompilerSpecError(UnsatisfiableSpecError):
+
     """Raised when a spec comiler conflicts with package constraints."""
+
     def __init__(self, provided, required):
         super(UnsatisfiableCompilerSpecError, self).__init__(
             provided, required, "compiler")
 
 
 class UnsatisfiableVariantSpecError(UnsatisfiableSpecError):
+
     """Raised when a spec variant conflicts with package constraints."""
+
     def __init__(self, provided, required):
         super(UnsatisfiableVariantSpecError, self).__init__(
             provided, required, "variant")
 
+
 class UnsatisfiableCompilerFlagSpecError(UnsatisfiableSpecError):
+
     """Raised when a spec variant conflicts with package constraints."""
+
     def __init__(self, provided, required):
         super(UnsatisfiableCompilerFlagSpecError, self).__init__(
             provided, required, "compiler_flags")
 
+
 class UnsatisfiableArchitectureSpecError(UnsatisfiableSpecError):
+
     """Raised when a spec architecture conflicts with package constraints."""
+
     def __init__(self, provided, required):
         super(UnsatisfiableArchitectureSpecError, self).__init__(
             provided, required, "architecture")
 
 
 class UnsatisfiableProviderSpecError(UnsatisfiableSpecError):
+
     """Raised when a provider is supplied but constraints don't match
        a vpkg requirement"""
+
     def __init__(self, provided, required):
         super(UnsatisfiableProviderSpecError, self).__init__(
             provided, required, "provider")
 
 # TODO: get rid of this and be more specific about particular incompatible
 # dep constraints
+
+
 class UnsatisfiableDependencySpecError(UnsatisfiableSpecError):
+
     """Raised when some dependency of constrained specs are incompatible"""
+
     def __init__(self, provided, required):
         super(UnsatisfiableDependencySpecError, self).__init__(
             provided, required, "dependency")
 
+
 class SpackYAMLError(spack.error.SpackError):
+
     def __init__(self, msg, yaml_error):
         super(SpackYAMLError, self).__init__(msg, str(yaml_error))
 
+
 class SpackRecordError(spack.error.SpackError):
+
     def __init__(self, msg):
         super(SpackRecordError, self).__init__(msg)
 
+
 class AmbiguousHashError(SpecError):
+
     def __init__(self, msg, *specs):
         super(AmbiguousHashError, self).__init__(msg)
         for spec in specs:
diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py
index 480e6290e7..97f142e746 100644
--- a/lib/spack/spack/test/__init__.py
+++ b/lib/spack/spack/test/__init__.py
@@ -39,7 +39,7 @@ test_names = ['architecture', 'versions', 'url_parse', 'url_substitution', 'pack
               'svn_fetch', 'hg_fetch', 'mirror', 'modules', 'url_extrapolate',
               'cc', 'link_tree', 'spec_yaml', 'optional_deps',
               'make_executable', 'configure_guess', 'lock', 'database',
-              'namespace_trie', 'yaml', 'sbang', 'environment',
+              'namespace_trie', 'yaml', 'sbang', 'environment', 'cmd.find',
               'cmd.uninstall', 'cmd.test_install']
 
 
diff --git a/lib/spack/spack/test/cmd/find.py b/lib/spack/spack/test/cmd/find.py
new file mode 100644
index 0000000000..371e9650e0
--- /dev/null
+++ b/lib/spack/spack/test/cmd/find.py
@@ -0,0 +1,60 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+
+import spack.cmd.find
+import unittest
+
+
+class Bunch(object):
+
+    def __init__(self, **kwargs):
+        self.__dict__.update(kwargs)
+
+
+class FindTest(unittest.TestCase):
+
+    def test_query_arguments(self):
+        query_arguments = spack.cmd.find.query_arguments
+        # Default arguments
+        args = Bunch(only_missing=False, missing=False,
+                     unknown=False, explicit=False, implicit=False)
+        q_args = query_arguments(args)
+        self.assertTrue('installed' in q_args)
+        self.assertTrue('known' in q_args)
+        self.assertTrue('explicit' in q_args)
+        self.assertEqual(q_args['installed'], True)
+        self.assertEqual(q_args['known'], any)
+        self.assertEqual(q_args['explicit'], any)
+        # Check that explicit works correctly
+        args.explicit = True
+        q_args = query_arguments(args)
+        self.assertEqual(q_args['explicit'], True)
+        args.explicit = False
+        args.implicit = True
+        q_args = query_arguments(args)
+        self.assertEqual(q_args['explicit'], False)
+        args.explicit = True
+        self.assertRaises(SystemExit, query_arguments, args)
diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 49dc971d3a..867d317e4d 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -25,8 +25,10 @@
 from spack import *
 import sys
 
+
 class Dealii(Package):
-    """C++ software library providing well-documented tools to build finite element codes for a broad variety of PDEs."""
+    """C++ software library providing well-documented tools to build finite
+    element codes for a broad variety of PDEs."""
     homepage = "https://www.dealii.org"
     url      = "https://github.com/dealii/dealii/releases/download/v8.4.0/dealii-8.4.0.tar.gz"
 
@@ -36,7 +38,7 @@ class Dealii(Package):
     variant('mpi',      default=True,  description='Compile with MPI')
     variant('arpack',   default=True,  description='Compile with Arpack and PArpack (only with MPI)')
     variant('doc',      default=False, description='Compile with documentation')
-    variant('gsl' ,     default=True,  description='Compile with GSL')
+    variant('gsl',      default=True,  description='Compile with GSL')
     variant('hdf5',     default=True,  description='Compile with HDF5 (only with MPI)')
     variant('metis',    default=True,  description='Compile with Metis')
     variant('netcdf',   default=True,  description='Compile with Netcdf (only with MPI)')
@@ -47,38 +49,40 @@ class Dealii(Package):
     variant('trilinos', default=True,  description='Compile with Trilinos (only with MPI)')
 
     # required dependencies, light version
-    depends_on ("blas")
-    # Boost 1.58 is blacklisted, see https://github.com/dealii/dealii/issues/1591
-    # require at least 1.59
-    depends_on ("boost@1.59.0:",     when='~mpi')
-    depends_on ("boost@1.59.0:+mpi", when='+mpi')
-    depends_on ("bzip2")
-    depends_on ("cmake")
-    depends_on ("lapack")
-    depends_on ("muparser")
-    depends_on ("suite-sparse")
-    depends_on ("tbb")
-    depends_on ("zlib")
+    depends_on("blas")
+    # Boost 1.58 is blacklisted, see
+    # https://github.com/dealii/dealii/issues/1591
+    # Require at least 1.59
+    depends_on("boost@1.59.0:+thread+system+serialization+iostreams",     when='~mpi')  # NOQA: ignore=E501
+    depends_on("boost@1.59.0:+mpi+thread+system+serialization+iostreams", when='+mpi')  # NOQA: ignore=E501
+    depends_on("bzip2")
+    depends_on("cmake")
+    depends_on("lapack")
+    depends_on("muparser")
+    depends_on("suite-sparse")
+    depends_on("tbb")
+    depends_on("zlib")
 
     # optional dependencies
-    depends_on ("mpi", when="+mpi")
-    depends_on ("arpack-ng+mpi", when='+arpack+mpi')
-    depends_on ("doxygen", when='+doc')
-    depends_on ("gsl", when='@8.5.0:+gsl')
-    depends_on ("gsl", when='@dev+gsl')
-    depends_on ("hdf5+mpi~cxx", when='+hdf5+mpi') #FIXME NetCDF declares dependency with ~cxx, why?
-    depends_on ("metis@5:", when='+metis')
-    depends_on ("netcdf+mpi", when="+netcdf+mpi")
-    depends_on ("netcdf-cxx", when='+netcdf+mpi')
-    depends_on ("oce", when='+oce')
-    depends_on ("p4est", when='+p4est+mpi')
-    depends_on ("petsc+mpi", when='+petsc+mpi')
-    depends_on ("slepc", when='+slepc+petsc+mpi')
-    depends_on ("trilinos", when='+trilinos+mpi')
+    depends_on("mpi",              when="+mpi")
+    depends_on("arpack-ng+mpi",    when='+arpack+mpi')
+    depends_on("doxygen+graphviz", when='+doc')
+    depends_on("graphviz",         when='+doc')
+    depends_on("gsl",              when='@8.5.0:+gsl')
+    depends_on("gsl",              when='@dev+gsl')
+    depends_on("hdf5+mpi",         when='+hdf5+mpi')
+    depends_on("metis@5:",         when='+metis')
+    depends_on("netcdf+mpi",       when="+netcdf+mpi")
+    depends_on("netcdf-cxx",       when='+netcdf+mpi')
+    depends_on("oce",              when='+oce')
+    depends_on("p4est",            when='+p4est+mpi')
+    depends_on("petsc+mpi",        when='+petsc+mpi')
+    depends_on("slepc",            when='+slepc+petsc+mpi')
+    depends_on("trilinos",         when='+trilinos+mpi')
 
     # developer dependnecies
-    depends_on ("numdiff", when='@dev')
-    depends_on ("astyle@2.04", when='@dev')
+    depends_on("numdiff",     when='@dev')
+    depends_on("astyle@2.04", when='@dev')
 
     def install(self, spec, prefix):
         options = []
@@ -96,17 +100,17 @@ class Dealii(Package):
             '-DDEAL_II_WITH_THREADS:BOOL=ON',
             '-DBOOST_DIR=%s' % spec['boost'].prefix,
             '-DBZIP2_DIR=%s' % spec['bzip2'].prefix,
-            # CMake's FindBlas/Lapack may pickup system's blas/lapack instead of Spack's.
-            # Be more specific to avoid this.
-            # Note that both lapack and blas are provided in -DLAPACK_XYZ variables
+            # CMake's FindBlas/Lapack may pickup system's blas/lapack instead
+            # of Spack's. Be more specific to avoid this.
+            # Note that both lapack and blas are provided in -DLAPACK_XYZ.
             '-DLAPACK_FOUND=true',
             '-DLAPACK_INCLUDE_DIRS=%s;%s' %
                 (spec['lapack'].prefix.include,
                  spec['blas'].prefix.include),
             '-DLAPACK_LIBRARIES=%s;%s' %
-                (join_path(spec['lapack'].prefix.lib,'liblapack.%s' % dsuf), # FIXME don't hardcode names
-                 join_path(spec['blas'].prefix.lib,'libblas.%s' % dsuf)),    # FIXME don't hardcode names
-            '-DMUPARSER_DIR=%s ' % spec['muparser'].prefix,
+                (spec['lapack'].lapack_shared_lib,
+                 spec['blas'].blas_shared_lib),
+            '-DMUPARSER_DIR=%s' % spec['muparser'].prefix,
             '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
             '-DTBB_DIR=%s' % spec['tbb'].prefix,
             '-DZLIB_DIR=%s' % spec['zlib'].prefix
@@ -116,33 +120,34 @@ class Dealii(Package):
         if '+mpi' in spec:
             options.extend([
                 '-DDEAL_II_WITH_MPI:BOOL=ON',
-                '-DCMAKE_C_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # FIXME: avoid hardcoding mpi wrappers names
-                '-DCMAKE_CXX_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
-                '-DCMAKE_Fortran_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
+                '-DCMAKE_C_COMPILER=%s'       % spec['mpi'].mpicc,
+                '-DCMAKE_CXX_COMPILER=%s'     % spec['mpi'].mpicxx,
+                '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
             ])
         else:
             options.extend([
                 '-DDEAL_II_WITH_MPI:BOOL=OFF',
             ])
 
-        # Optional dependencies for which librariy names are the same as CMake variables
-        for library in ('gsl','hdf5','p4est','petsc','slepc','trilinos','metis'):
+        # Optional dependencies for which librariy names are the same as CMake
+        # variables:
+        for library in ('gsl', 'hdf5', 'p4est', 'petsc', 'slepc', 'trilinos', 'metis'):  # NOQA: ignore=E501
             if library in spec:
                 options.extend([
-                    '-D{library}_DIR={value}'.format(library=library.upper(), value=spec[library].prefix),
-                    '-DDEAL_II_WITH_{library}:BOOL=ON'.format(library=library.upper())
+                    '-D%s_DIR=%s' % (library.upper(), spec[library].prefix),
+                    '-DDEAL_II_WITH_%s:BOOL=ON' % library.upper()
                 ])
             else:
                 options.extend([
-                    '-DDEAL_II_WITH_{library}:BOOL=OFF'.format(library=library.upper())
+                    '-DDEAL_II_WITH_%s:BOOL=OFF' % library.upper()
                 ])
 
         # doxygen
         options.extend([
-            '-DDEAL_II_COMPONENT_DOCUMENTATION=%s' % ('ON' if '+doc' in spec else 'OFF'),
+            '-DDEAL_II_COMPONENT_DOCUMENTATION=%s' %
+            ('ON' if '+doc' in spec else 'OFF'),
         ])
 
-
         # arpack
         if '+arpack' in spec:
             options.extend([
@@ -160,11 +165,13 @@ class Dealii(Package):
             options.extend([
                 '-DNETCDF_FOUND=true',
                 '-DNETCDF_LIBRARIES=%s;%s' %
-                    (join_path(spec['netcdf-cxx'].prefix.lib,'libnetcdf_c++.%s' % dsuf),
-                    join_path(spec['netcdf'].prefix.lib,'libnetcdf.%s' % dsuf)),
+                    (join_path(spec['netcdf-cxx'].prefix.lib,
+                               'libnetcdf_c++.%s' % dsuf),
+                     join_path(spec['netcdf'].prefix.lib,
+                               'libnetcdf.%s' % dsuf)),
                 '-DNETCDF_INCLUDE_DIRS=%s;%s' %
                     (spec['netcdf-cxx'].prefix.include,
-                    spec['netcdf'].prefix.include),
+                     spec['netcdf'].prefix.include),
             ])
         else:
             options.extend([
@@ -200,7 +207,7 @@ class Dealii(Package):
         with working_dir('examples/step-3'):
             cmake('.')
             make('release')
-            make('run',parallel=False)
+            make('run', parallel=False)
 
         # An example which uses Metis + PETSc
         # FIXME: switch step-18 to MPI
@@ -213,7 +220,7 @@ class Dealii(Package):
             if '^petsc' in spec and '^metis' in spec:
                 cmake('.')
                 make('release')
-                make('run',parallel=False)
+                make('run', parallel=False)
 
         # take step-40 which can use both PETSc and Trilinos
         # FIXME: switch step-40 to MPI run
@@ -222,43 +229,49 @@ class Dealii(Package):
             print('========== Step-40 PETSc ============')
             print('=====================================')
             # list the number of cycles to speed up
-            filter_file(r'(const unsigned int n_cycles = 8;)',  ('const unsigned int n_cycles = 2;'), 'step-40.cc')
+            filter_file(r'(const unsigned int n_cycles = 8;)',
+                        ('const unsigned int n_cycles = 2;'), 'step-40.cc')
             cmake('.')
             if '^petsc' in spec:
                 make('release')
-                make('run',parallel=False)
+                make('run', parallel=False)
 
             print('=====================================')
             print('========= Step-40 Trilinos ==========')
             print('=====================================')
             # change Linear Algebra to Trilinos
-            filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)',  ('#define FORCE_USE_OF_TRILINOS'), 'step-40.cc')
+            filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)',
+                        ('#define FORCE_USE_OF_TRILINOS'), 'step-40.cc')
             if '^trilinos+hypre' in spec:
                 make('release')
-                make('run',parallel=False)
+                make('run', parallel=False)
 
             print('=====================================')
             print('=== Step-40 Trilinos SuperluDist ====')
             print('=====================================')
             # change to direct solvers
-            filter_file(r'(LA::SolverCG solver\(solver_control\);)',  ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc')
-            filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)',  (''), 'step-40.cc')
-            filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)',  (''), 'step-40.cc')
-            filter_file(r'(preconditioner.initialize\(system_matrix, data\);)',  (''), 'step-40.cc')
-            filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)',  ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc')
+            filter_file(r'(LA::SolverCG solver\(solver_control\);)',  ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc')  # NOQA: ignore=E501
+            filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)',
+                        (''), 'step-40.cc')
+            filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)',
+                        (''), 'step-40.cc')
+            filter_file(r'(preconditioner.initialize\(system_matrix, data\);)',
+                        (''), 'step-40.cc')
+            filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)',  ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc')  # NOQA: ignore=E501
             filter_file(r'(preconditioner\);)',  (''), 'step-40.cc')
             if '^trilinos+superlu-dist' in spec:
                 make('release')
-                make('run',paralle=False)
+                make('run', paralle=False)
 
             print('=====================================')
             print('====== Step-40 Trilinos MUMPS =======')
             print('=====================================')
             # switch to Mumps
-            filter_file(r'(Amesos_Superludist)',  ('Amesos_Mumps'), 'step-40.cc')
+            filter_file(r'(Amesos_Superludist)',
+                        ('Amesos_Mumps'), 'step-40.cc')
             if '^trilinos+mumps' in spec:
                 make('release')
-                make('run',parallel=False)
+                make('run', parallel=False)
 
         print('=====================================')
         print('============ Step-36 ================')
@@ -267,7 +280,7 @@ class Dealii(Package):
             if 'slepc' in spec:
                 cmake('.')
                 make('release')
-                make('run',parallel=False)
+                make('run', parallel=False)
 
         print('=====================================')
         print('============ Step-54 ================')
@@ -276,7 +289,7 @@ class Dealii(Package):
             if 'oce' in spec:
                 cmake('.')
                 make('release')
-                make('run',parallel=False)
+                make('run', parallel=False)
 
     def setup_environment(self, spack_env, env):
         env.set('DEAL_II_DIR', self.prefix)
diff --git a/var/spack/repos/builtin/packages/launchmon/package.py b/var/spack/repos/builtin/packages/launchmon/package.py
index f38bc38202..f256810005 100644
--- a/var/spack/repos/builtin/packages/launchmon/package.py
+++ b/var/spack/repos/builtin/packages/launchmon/package.py
@@ -24,29 +24,19 @@
 ##############################################################################
 from spack import *
 
+
 class Launchmon(Package):
     """Software infrastructure that enables HPC run-time tools to
        co-locate tool daemons with a parallel job."""
-    homepage = "http://sourceforge.net/projects/launchmon"
-    url      = "http://downloads.sourceforge.net/project/launchmon/launchmon/1.0.1%20release/launchmon-1.0.1.tar.gz"
+    homepage = "https://github.com/LLNL/LaunchMON"
+    url      = "https://github.com/LLNL/LaunchMON/releases/download/v1.0.2/launchmon-v1.0.2.tar.gz"  # NOQA: ignore=E501
 
-    version('1.0.1', '2f12465803409fd07f91174a4389eb2b')
-    version('1.0.1-2', git='https://github.com/llnl/launchmon.git', commit='ff7e22424b8f375318951eb1c9282fcbbfa8aadf')
+    version('1.0.2', '8d6ba77a0ec2eff2fde2c5cc8fa7ff7a')
 
     depends_on('autoconf')
     depends_on('automake')
     depends_on('libtool')
 
-
-    def patch(self):
-        # This patch makes libgcrypt compile correctly with newer gcc versions.
-        mf = FileFilter('tools/libgcrypt/tests/Makefile.in')
-        mf.filter(r'(basic_LDADD\s*=\s*.*)',     r'\1 -lgpg-error')
-        mf.filter(r'(tsexp_LDADD\s*=\s*.*)',     r'\1 -lgpg-error')
-        mf.filter(r'(keygen_LDADD\s*=\s*.*)',    r'\1 -lgpg-error')
-        mf.filter(r'(benchmark_LDADD\s*=\s*.*)', r'\1 -lgpg-error')
-
-
     def install(self, spec, prefix):
         configure(
             "--prefix=" + prefix,
diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index c090c131c6..c32f66590a 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -23,7 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os, shutil
+import os, glob
 
 
 class Llvm(Package):
@@ -46,7 +46,9 @@ class Llvm(Package):
     variant('libcxx', default=True, description="Build the LLVM C++ standard library")
     variant('compiler-rt', default=True, description="Build the LLVM compiler runtime, including sanitizers")
     variant('gold', default=True, description="Add support for LTO with the gold linker plugin")
-
+    variant('shared_libs', default=False, description="Build all components as shared libraries, faster, less memory to build, less stable")
+    variant('link_dylib', default=False, description="Build and link the libLLVM shared library rather than static")
+    variant('all_targets', default=True, description="Build all supported targets, default targets <current arch>,NVPTX,AMDGPU,CppBackend")
 
     # Build dependency
     depends_on('cmake @2.8.12.2:')
@@ -257,6 +259,28 @@ class Llvm(Package):
         if '+compiler-rt' not in spec:
             cmake_args.append('-DLLVM_EXTERNAL_COMPILER_RT_BUILD:Bool=OFF')
 
+        if '+shared_libs' in spec:
+            cmake_args.append('-DBUILD_SHARED_LIBS:Bool=ON')
+
+        if '+link_dylib' in spec:
+            cmake_args.append('-DLLVM_LINK_LLVM_DYLIB:Bool=ON')
+
+        if '+all_targets' not in spec: # all is default on cmake
+            targets = ['CppBackend', 'NVPTX', 'AMDGPU']
+            if 'x86' in spec.architecture.lower():
+                targets.append('X86')
+            elif 'arm' in spec.architecture.lower():
+                targets.append('ARM')
+            elif 'aarch64' in spec.architecture.lower():
+                targets.append('AArch64')
+            elif 'sparc' in spec.architecture.lower():
+                targets.append('sparc')
+            elif ('ppc' in spec.architecture.lower() or
+                  'power' in spec.architecture.lower()):
+                targets.append('PowerPC')
+
+            cmake_args.append('-DLLVM_TARGETS_TO_BUILD:Bool=' + ';'.join(targets))
+
         if  '+clang' not in spec:
             if '+clang_extra' in spec:
                 raise SpackException('The clang_extra variant requires the clang variant to be selected')
@@ -267,7 +291,5 @@ class Llvm(Package):
             cmake(*cmake_args)
             make()
             make("install")
-            query_path = os.path.join('bin', 'clang-query')
-            # Manually install clang-query, because llvm doesn't...
-            if os.path.exists(query_path):
-                shutil.copy(query_path, os.path.join(prefix, 'bin'))
+            cp = which('cp')
+            cp('-a', 'bin/', prefix)
diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index 061179b78e..c4f2afaff2 100644
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -24,55 +24,61 @@
 ##############################################################################
 
 from spack import *
-import glob, sys, os
+import glob
+import sys
+import os
+
 
 class Metis(Package):
-    """
-    METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill
-    reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel
-    recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
-    """
+    """METIS is a set of serial programs for partitioning graphs, partitioning
+       finite element meshes, and producing fill reducing orderings for sparse
+       matrices. The algorithms implemented in METIS are based on the
+       multilevel recursive-bisection, multilevel k-way, and multi-constraint
+       partitioning schemes."""
 
-    homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview'
-    url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz"
+    homepage = "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview"
+    base_url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis"
 
-    version('5.1.0', '5465e67079419a69e0116de24fce58fe',
-            url='http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz')
-    version('4.0.3', '5efa35de80703c1b2c4d0de080fafbcf4e0d363a21149a1ad2f96e0144841a55',
-            url='http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD/metis-4.0.3.tar.gz')
+    version('5.1.0', '5465e67079419a69e0116de24fce58fe')
+    version('5.0.2', 'acb521a4e8c2e6dd559a7f9abd0468c5')
+    version('4.0.3', 'd3848b454532ef18dc83e4fb160d1e10')
 
     variant('shared', default=True, description='Enables the build of shared libraries')
     variant('debug', default=False, description='Builds the library in debug mode')
     variant('gdb', default=False, description='Enables gdb support')
 
     variant('idx64', default=False, description='Use int64_t as default index type')
-    variant('double', default=False, description='Use double precision floating point types')
+    variant('real64', default=False, description='Use double precision floating point types')
 
-    depends_on('cmake @2.8:', when='@5:')  # build-time dependency
-    depends_on('gdb', when='+gdb')
+    depends_on('cmake@2.8:', when='@5:')  # build-time dependency
 
     patch('install_gklib_defs_rename.patch', when='@5:')
 
+    def url_for_version(self, version):
+        verdir = 'OLD/' if version < Version('4.0.3') else ''
+        return '%s/%smetis-%s.tar.gz' % (Metis.base_url, verdir, version)
 
-    @when('@4:4.0.3')
+    @when('@:4')
     def install(self, spec, prefix):
-
-        if '+gdb' in spec:
-            raise InstallError('gdb support not implemented in METIS 4!')
-        if '+idx64' in spec:
-            raise InstallError('idx64 option not implemented in METIS 4!')
-        if '+double' in spec:
-            raise InstallError('double option not implemented for METIS 4!')
+        # Process library spec and options
+        unsupp_vars = [v for v in ('+gdb', '+idx64', '+real64') if v in spec]
+        if unsupp_vars:
+            msg = 'Given variants %s are unsupported by METIS 4!' % unsupp_vars
+            raise InstallError(msg)
 
         options = ['COPTIONS=-fPIC']
         if '+debug' in spec:
             options.append('OPTFLAGS=-g -O0')
         make(*options)
 
+        # Compile and install library files
+        ccompile = Executable(self.compiler.cc)
+
         mkdir(prefix.bin)
-        for x in ('pmetis', 'kmetis', 'oemetis', 'onmetis', 'partnmesh',
-                  'partdmesh', 'mesh2nodal', 'mesh2dual', 'graphchk'):
-            install(x, prefix.bin)
+        binfiles = ('pmetis', 'kmetis', 'oemetis', 'onmetis', 'partnmesh',
+                    'partdmesh', 'mesh2nodal', 'mesh2dual', 'graphchk')
+        for binfile in binfiles:
+            install(binfile, prefix.bin)
 
         mkdir(prefix.lib)
         install('libmetis.a', prefix.lib)
@@ -82,106 +88,120 @@ class Metis(Package):
             install(h, prefix.include)
 
         mkdir(prefix.share)
-        for f in (join_path(*p)
-                  for p in (('Programs', 'io.c'),
-                            ('Test','mtest.c'),
-                            ('Graphs','4elt.graph'),
-                            ('Graphs', 'metis.mesh'),
-                            ('Graphs', 'test.mgraph'))):
-            install(f, prefix.share)
+        sharefiles = (('Graphs', '4elt.graph'), ('Graphs', 'metis.mesh'),
+                      ('Graphs', 'test.mgraph'))
+        for sharefile in tuple(join_path(*sf) for sf in sharefiles):
+            install(sharefile, prefix.share)
 
         if '+shared' in spec:
+            shared_flags = ['-fPIC', '-shared']
             if sys.platform == 'darwin':
-                lib_dsuffix = 'dylib'
-                load_flag = '-Wl,-all_load'
-                no_load_flag = ''
+                shared_suffix = 'dylib'
+                shared_flags.extend(['-Wl,-all_load', 'libmetis.a'])
             else:
-                lib_dsuffix = 'so'
-                load_flag = '-Wl,-whole-archive'
-                no_load_flag = '-Wl,-no-whole-archive'
+                shared_suffix = 'so'
+                shared_flags.extend(['-Wl,-whole-archive', 'libmetis.a',
+                                     '-Wl,-no-whole-archive'])
 
-            os.system(spack_cc + ' -fPIC -shared ' + load_flag +
-                      ' libmetis.a ' + no_load_flag + ' -o libmetis.' +
-                      lib_dsuffix)
-            install('libmetis.' + lib_dsuffix, prefix.lib)
+            shared_out = '%s/libmetis.%s' % (prefix.lib, shared_suffix)
+            shared_flags.extend(['-o', shared_out])
 
-        # Set up and run tests on installation
-        symlink(join_path(prefix.share, 'io.c'), 'io.c')
-        symlink(join_path(prefix.share, 'mtest.c'), 'mtest.c')
-        os.system(spack_cc + ' -I%s' % prefix.include + ' -c io.c')
-        os.system(spack_cc + ' -I%s' % prefix.include +
-                  ' -L%s' % prefix.lib + ' -lmetis mtest.c io.o -o mtest')
-        _4eltgraph = join_path(prefix.share, '4elt.graph')
-        test_mgraph = join_path(prefix.share, 'test.mgraph')
-        metis_mesh = join_path(prefix.share, 'metis.mesh')
-        kmetis = join_path(prefix.bin, 'kmetis')
-        os.system('./mtest ' + _4eltgraph)
-        os.system(kmetis + ' ' + _4eltgraph + ' 40')
-        os.system(join_path(prefix.bin, 'onmetis') + ' ' + _4eltgraph)
-        os.system(join_path(prefix.bin, 'pmetis') + ' ' + test_mgraph + ' 2')
-        os.system(kmetis + ' ' + test_mgraph + ' 2')
-        os.system(kmetis + ' ' + test_mgraph + ' 5')
-        os.system(join_path(prefix.bin, 'partnmesh') + metis_mesh + ' 10')
-        os.system(join_path(prefix.bin, 'partdmesh') + metis_mesh + ' 10')
-        os.system(join_path(prefix.bin, 'mesh2dual') + metis_mesh)
+            ccompile(*shared_flags)
 
+        # Set up and run tests on installation
+        ccompile('-I%s' % prefix.include, '-L%s' % prefix.lib,
+                 '-Wl,-rpath=%s' % (prefix.lib if '+shared' in spec else ''),
+                 join_path('Programs', 'io.o'), join_path('Test', 'mtest.c'),
+                 '-o', '%s/mtest' % prefix.bin, '-lmetis', '-lm')
+
+        test_bin = lambda testname: join_path(prefix.bin, testname)
+        test_graph = lambda graphname: join_path(prefix.share, graphname)
+
+        graph = test_graph('4elt.graph')
+        os.system('%s %s' % (test_bin('mtest'), graph))
+        os.system('%s %s 40' % (test_bin('kmetis'), graph))
+        os.system('%s %s' % (test_bin('onmetis'), graph))
+        graph = test_graph('test.mgraph')
+        os.system('%s %s 2' % (test_bin('pmetis'), graph))
+        os.system('%s %s 2' % (test_bin('kmetis'), graph))
+        os.system('%s %s 5' % (test_bin('kmetis'), graph))
+        graph = test_graph('metis.mesh')
+        os.system('%s %s 10' % (test_bin('partnmesh'), graph))
+        os.system('%s %s 10' % (test_bin('partdmesh'), graph))
+        os.system('%s %s' % (test_bin('mesh2dual'), graph))
+
+        # FIXME: The following code should replace the testing code in the
+        # block above since it causes installs to fail when one or more of the
+        # Metis tests fail, but it currently doesn't work because the 'mtest',
+        # 'onmetis', and 'partnmesh' tests return error codes that trigger
+        # false positives for failure.
+        """
+        Executable(test_bin('mtest'))(test_graph('4elt.graph'))
+        Executable(test_bin('kmetis'))(test_graph('4elt.graph'), '40')
+        Executable(test_bin('onmetis'))(test_graph('4elt.graph'))
+
+        Executable(test_bin('pmetis'))(test_graph('test.mgraph'), '2')
+        Executable(test_bin('kmetis'))(test_graph('test.mgraph'), '2')
+        Executable(test_bin('kmetis'))(test_graph('test.mgraph'), '5')
+
+        Executable(test_bin('partnmesh'))(test_graph('metis.mesh'), '10')
+        Executable(test_bin('partdmesh'))(test_graph('metis.mesh'), '10')
+        Executable(test_bin('mesh2dual'))(test_graph('metis.mesh'))
+        """
 
     @when('@5:')
     def install(self, spec, prefix):
-
         options = []
         options.extend(std_cmake_args)
 
         build_directory = join_path(self.stage.path, 'spack-build')
         source_directory = self.stage.source_path
 
-        options.append('-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=source_directory))
+        options.append('-DGKLIB_PATH:PATH=%s/GKlib' % source_directory)
         options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
 
         if '+shared' in spec:
             options.append('-DSHARED:BOOL=ON')
-
         if '+debug' in spec:
             options.extend(['-DDEBUG:BOOL=ON',
                             '-DCMAKE_BUILD_TYPE:STRING=Debug'])
-
         if '+gdb' in spec:
             options.append('-DGDB:BOOL=ON')
 
         metis_header = join_path(source_directory, 'include', 'metis.h')
-
         if '+idx64' in spec:
             filter_file('IDXTYPEWIDTH 32', 'IDXTYPEWIDTH 64', metis_header)
-
-        if '+double' in spec:
+        if '+real64' in spec:
             filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header)
 
         # Make clang 7.3 happy.
         # Prevents "ld: section __DATA/__thread_bss extends beyond end of file"
         # See upstream LLVM issue https://llvm.org/bugs/show_bug.cgi?id=27059
-        # Adopted from https://github.com/Homebrew/homebrew-science/blob/master/metis.rb
+        # and https://github.com/Homebrew/homebrew-science/blob/master/metis.rb
         if spec.satisfies('%clang@7.3.0'):
-            filter_file('#define MAX_JBUFS 128', '#define MAX_JBUFS 24', join_path(source_directory, 'GKlib', 'error.c'))
+            filter_file('#define MAX_JBUFS 128', '#define MAX_JBUFS 24',
+                        join_path(source_directory, 'GKlib', 'error.c'))
 
         with working_dir(build_directory, create=True):
             cmake(source_directory, *options)
             make()
-            make("install")
+            make('install')
+
             # now run some tests:
-            for f in ["4elt", "copter2", "mdual"]:
-                graph = join_path(source_directory,'graphs','%s.graph' % f)
-                Executable(join_path(prefix.bin,'graphchk'))(graph)
-                Executable(join_path(prefix.bin,'gpmetis'))(graph,'2')
-                Executable(join_path(prefix.bin,'ndmetis'))(graph)
+            for f in ['4elt', 'copter2', 'mdual']:
+                graph = join_path(source_directory, 'graphs', '%s.graph' % f)
+                Executable(join_path(prefix.bin, 'graphchk'))(graph)
+                Executable(join_path(prefix.bin, 'gpmetis'))(graph, '2')
+                Executable(join_path(prefix.bin, 'ndmetis'))(graph)
 
-            graph = join_path(source_directory,'graphs','test.mgraph')
-            Executable(join_path(prefix.bin,'gpmetis'))(graph,'2')
-            graph = join_path(source_directory,'graphs','metis.mesh')
-            Executable(join_path(prefix.bin,'mpmetis'))(graph,'2')
+            graph = join_path(source_directory, 'graphs', 'test.mgraph')
+            Executable(join_path(prefix.bin, 'gpmetis'))(graph, '2')
+            graph = join_path(source_directory, 'graphs', 'metis.mesh')
+            Executable(join_path(prefix.bin, 'mpmetis'))(graph, '2')
 
             # install GKlib headers, which will be needed for ParMETIS
-            GKlib_dist = join_path(prefix.include,'GKlib')
+            GKlib_dist = join_path(prefix.include, 'GKlib')
             mkdirp(GKlib_dist)
-            fs = glob.glob(join_path(source_directory,'GKlib',"*.h"))
-            for f in fs:
-                install(f, GKlib_dist)
+            hfiles = glob.glob(join_path(source_directory, 'GKlib', '*.h'))
+            for hfile in hfiles:
+                install(hfile, GKlib_dist)
diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py
index 17c7ff82f4..72ff0ee6fc 100644
--- a/var/spack/repos/builtin/packages/octave/package.py
+++ b/var/spack/repos/builtin/packages/octave/package.py
@@ -23,6 +23,8 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+import sys
+
 
 class Octave(Package):
     """GNU Octave is a high-level language, primarily intended for numerical
@@ -34,7 +36,8 @@ class Octave(Package):
     homepage = "https://www.gnu.org/software/octave/"
     url      = "ftp://ftp.gnu.org/gnu/octave/octave-4.0.0.tar.gz"
 
-    version('4.0.0' , 'a69f8320a4f20a8480c1b278b1adb799')
+    version('4.0.2', 'c2a5cacc6e4c52f924739cdf22c2c687')
+    version('4.0.0', 'a69f8320a4f20a8480c1b278b1adb799')
 
     # Variants
     variant('readline',   default=True)
@@ -62,33 +65,35 @@ class Octave(Package):
     # Required dependencies
     depends_on('blas')
     depends_on('lapack')
+    # Octave does not configure with sed from darwin:
+    depends_on('sed', sys.platform == 'darwin')
     depends_on('pcre')
+    depends_on('pkg-config')
 
     # Strongly recommended dependencies
-    depends_on('readline',    when='+readline')
+    depends_on('readline',     when='+readline')
 
     # Optional dependencies
-    depends_on('arpack',      when='+arpack')
-    depends_on('curl',        when='+curl')
-    depends_on('fftw',      when='+fftw')
-    depends_on('fltk',        when='+fltk')
-    depends_on('fontconfig',  when='+fontconfig')
-    depends_on('freetype',    when='+freetype')
-    depends_on('glpk',        when='+glpk')
-    depends_on('gl2ps',       when='+gl2ps')
-    depends_on('gnuplot',     when='+gnuplot')
-    depends_on('ImageMagick', when='+magick')
-    depends_on('hdf5',        when='+hdf5')
-    depends_on('jdk',         when='+jdk')
-    depends_on('llvm',        when='+llvm')
-    #depends_on('opengl',      when='+opengl')    # TODO: add package
-    depends_on('qhull',       when='+qhull')
-    depends_on('qrupdate',    when='+qrupdate')
-    #depends_on('qscintilla',  when='+qscintilla) # TODO: add package
-    depends_on('qt',          when='+qt')
-    depends_on('suite-sparse',when='+suitesparse')
-    depends_on('zlib',        when='+zlib')
-
+    depends_on('arpack',       when='+arpack')
+    depends_on('curl',         when='+curl')
+    depends_on('fftw',         when='+fftw')
+    depends_on('fltk',         when='+fltk')
+    depends_on('fontconfig',   when='+fontconfig')
+    depends_on('freetype',     when='+freetype')
+    depends_on('glpk',         when='+glpk')
+    depends_on('gl2ps',        when='+gl2ps')
+    depends_on('gnuplot',      when='+gnuplot')
+    depends_on('ImageMagick',  when='+magick')
+    depends_on('hdf5',         when='+hdf5')
+    depends_on('jdk',          when='+jdk')
+    depends_on('llvm',         when='+llvm')
+    # depends_on('opengl',      when='+opengl')    # TODO: add package
+    depends_on('qhull',        when='+qhull')
+    depends_on('qrupdate',     when='+qrupdate')
+    # depends_on('qscintilla',  when='+qscintilla) # TODO: add package
+    depends_on('qt',           when='+qt')
+    depends_on('suite-sparse', when='+suitesparse')
+    depends_on('zlib',         when='+zlib')
 
     def install(self, spec, prefix):
         config_args = [
@@ -154,7 +159,8 @@ class Octave(Package):
             config_args.append("--without-glpk")
 
         if '+magick' in spec:
-            config_args.append("--with-magick=%s" % spec['ImageMagick'].prefix.lib)
+            config_args.append("--with-magick=%s"
+                               % spec['ImageMagick'].prefix.lib)
 
         if '+hdf5' in spec:
             config_args.extend([
@@ -187,7 +193,8 @@ class Octave(Package):
 
         if '+qrupdate' in spec:
             config_args.extend([
-                "--with-qrupdate-includedir=%s" % spec['qrupdate'].prefix.include,
+                "--with-qrupdate-includedir=%s"
+                % spec['qrupdate'].prefix.include,
                 "--with-qrupdate-libdir=%s"     % spec['qrupdate'].prefix.lib
             ])
         else:
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 0e3185db25..4e465e1784 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -27,6 +27,26 @@ import os
 from spack import *
 
 
+def _verbs_dir():
+    """
+    Try to find the directory where the OpenFabrics verbs package is
+    installed. Return None if not found.
+    """
+    try:
+        # Try to locate Verbs by looking for a utility in the path
+        ibv_devices = which("ibv_devices")
+        # Run it (silently) to ensure it works
+        ibv_devices(output=str, error=str)
+        # Get path to executable
+        path = ibv_devices.exe[0]
+        # Remove executable name and "bin" directory
+        path = os.path.dirname(path)
+        path = os.path.dirname(path)
+        return path
+    except:
+        return None
+
+
 class Openmpi(Package):
     """Open MPI is a project combining technologies and resources from
        several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI)
@@ -54,7 +74,7 @@ class Openmpi(Package):
     variant('psm', default=False, description='Build support for the PSM library.')
     variant('psm2', default=False, description='Build support for the Intel PSM2 library.')
     variant('pmi', default=False, description='Build support for PMI-based launchers')
-    variant('verbs', default=False, description='Build support for OpenFabrics verbs.')
+    variant('verbs', default=_verbs_dir() is not None, description='Build support for OpenFabrics verbs.')
     variant('mxm', default=False, description='Build Mellanox Messaging support')
 
     variant('thread_multiple', default=False, description='Enable MPI_THREAD_MULTIPLE support')
@@ -113,7 +133,6 @@ class Openmpi(Package):
             # Fabrics
             '--with-psm' if '+psm' in spec else '--without-psm',
             '--with-psm2' if '+psm2' in spec else '--without-psm2',
-            ('--with-%s' % self.verbs) if '+verbs' in spec else ('--without-%s' % self.verbs),
             '--with-mxm' if '+mxm' in spec else '--without-mxm',
             # Other options
             '--enable-mpi-thread-multiple' if '+thread_multiple' in spec else '--disable-mpi-thread-multiple',
@@ -121,6 +140,14 @@ class Openmpi(Package):
             '--with-sqlite3' if '+sqlite3' in spec else '--without-sqlite3',
             '--enable-vt' if '+vt' in spec else '--disable-vt'
         ])
+        if '+verbs' in spec:
+            path = _verbs_dir()
+            if path is not None:
+                config_args.append('--with-%s=%s' % (self.verbs, path))
+            else:
+                config_args.append('--with-%s' % self.verbs)
+        else:
+            config_args.append('--without-%s' % self.verbs)
 
         # TODO: use variants for this, e.g. +lanl, +llnl, etc.
         # use this for LANL builds, but for LLNL builds, we need:
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index 2dead4a76a..9b36f273e4 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -26,33 +26,36 @@
 from spack import *
 import sys
 
+
 class Parmetis(Package):
-    """
-    ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured
-    graphs, meshes, and for computing fill-reducing orderings of sparse matrices.
-    """
+    """ParMETIS is an MPI-based parallel library that implements a variety of
+       algorithms for partitioning unstructured graphs, meshes, and for
+       computing fill-reducing orderings of sparse matrices."""
+
     homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview'
-    url = 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz'
+    base_url = 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis'
 
     version('4.0.3', 'f69c479586bf6bb7aff6a9bc0c739628')
+    version('4.0.2', '0912a953da5bb9b5e5e10542298ffdce')
 
     variant('shared', default=True, description='Enables the build of shared libraries')
     variant('debug', default=False, description='Builds the library in debug mode')
     variant('gdb', default=False, description='Enables gdb support')
 
-    depends_on('cmake @2.8:')  # build dependency
+    depends_on('cmake@2.8:')  # build dependency
     depends_on('mpi')
-
-    patch('enable_external_metis.patch')
     depends_on('metis@5:')
 
+    patch('enable_external_metis.patch')
     # bug fixes from PETSc developers
-    # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/
+    # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/  # NOQA: ignore=E501
     patch('pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch')
-    # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/
+    # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/  # NOQA: ignore=E501
     patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')
 
-    depends_on('gdb', when='+gdb')
+    def url_for_version(self, version):
+        verdir = 'OLD/' if version < Version('3.2.0') else ''
+        return '%s/%sparmetis-%s.tar.gz' % (Parmetis.base_url, verdir, version)
 
     def install(self, spec, prefix):
         options = []
@@ -60,30 +63,27 @@ class Parmetis(Package):
 
         build_directory = join_path(self.stage.path, 'spack-build')
         source_directory = self.stage.source_path
-        metis_source = join_path(source_directory, 'metis')
 
-        # FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case
-        # FIXME : they use a non-standard name
-        options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=spec['metis'].prefix.include),
-                        '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=spec['metis'].prefix),
-                        '-DCMAKE_C_COMPILER:STRING=mpicc',
-                        '-DCMAKE_CXX_COMPILER:STRING=mpicxx'])
+        options.extend([
+            '-DGKLIB_PATH:PATH=%s/GKlib' % spec['metis'].prefix.include,
+            '-DMETIS_PATH:PATH=%s' % spec['metis'].prefix,
+            '-DCMAKE_C_COMPILER:STRING=%s' % spec['mpi'].mpicc,
+            '-DCMAKE_CXX_COMPILER:STRING=%s' % spec['mpi'].mpicxx
+        ])
 
         if '+shared' in spec:
             options.append('-DSHARED:BOOL=ON')
-
         if '+debug' in spec:
             options.extend(['-DDEBUG:BOOL=ON',
                             '-DCMAKE_BUILD_TYPE:STRING=Debug'])
-
         if '+gdb' in spec:
             options.append('-DGDB:BOOL=ON')
 
         with working_dir(build_directory, create=True):
             cmake(source_directory, *options)
             make()
-            make("install")
+            make('install')
 
-            # The shared library is not installed correctly on Darwin; correct this
+            # The shared library is not installed correctly on Darwin; fix this
             if (sys.platform == 'darwin') and ('+shared' in spec):
                 fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/py-autopep8/package.py b/var/spack/repos/builtin/packages/py-autopep8/package.py
new file mode 100644
index 0000000000..f2fd3cd683
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-autopep8/package.py
@@ -0,0 +1,16 @@
+from spack import *
+
+class PyAutopep8(Package):
+    """Automatic pep8 formatter"""
+    homepage = "https://github.com/hhatto/autopep8"
+    url      = "https://github.com/hhatto/autopep8/archive/ver1.2.2.tar.gz"
+
+    version('1.2.2', 'def3d023fc9dfd1b7113602e965ad8e1')
+
+    extends('python')
+    depends_on('py-setuptools')
+    depends_on('py-pep8')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
+
diff --git a/var/spack/repos/builtin/packages/py-pep8/package.py b/var/spack/repos/builtin/packages/py-pep8/package.py
new file mode 100644
index 0000000000..987783b392
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pep8/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class PyPep8(Package):
+    """python pep8 format checker"""
+    homepage = "https://github.com/PyCQA/pycodestyle"
+    url      = "https://github.com/PyCQA/pycodestyle/archive/1.7.0.tar.gz"
+
+    version('1.7.0', '31070a3a6391928893cbf5fa523eb8d9')
+
+    extends('python')
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
+
diff --git a/var/spack/repos/builtin/packages/rust-bindgen/package.py b/var/spack/repos/builtin/packages/rust-bindgen/package.py
new file mode 100644
index 0000000000..854016d12a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rust-bindgen/package.py
@@ -0,0 +1,18 @@
+from spack import *
+import os
+
+
+class RustBindgen(Package):
+    """The rust programming language toolchain"""
+    homepage = "http://www.rust-lang.org"
+    url = "https://github.com/crabtw/rust-bindgen"
+
+    version('0.16', tag='0.16', git='https://github.com/crabtw/rust-bindgen')
+
+    extends("rust")
+    depends_on("llvm")
+
+    def install(self, spec, prefix):
+        env = dict(os.environ)
+        env['LIBCLANG_PATH'] = os.path.join(spec['llvm'].prefix, 'lib')
+        cargo('install', '--root', prefix, env=env)
diff --git a/var/spack/repos/builtin/packages/rust/package.py b/var/spack/repos/builtin/packages/rust/package.py
new file mode 100644
index 0000000000..65f81ce534
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rust/package.py
@@ -0,0 +1,63 @@
+from spack import *
+import os
+
+
+def get_submodules():
+    git = which('git')
+    git('submodule', 'update', '--init', '--recursive')
+
+class Rust(Package):
+    """The rust programming language toolchain"""
+    homepage = "http://www.rust-lang.org"
+    url = "https://github.com/rust-lang/rust"
+
+    version('1.8.0', tag='1.8.0', git="https://github.com/rust-lang/rust")
+
+    resource(name='cargo',
+             git="https://github.com/rust-lang/cargo.git",
+             tag='0.10.0',
+             destination='cargo')
+
+    extendable = True
+
+    # Rust
+    depends_on("llvm")
+    depends_on("curl")
+    depends_on("git")
+    depends_on("cmake")
+    depends_on("python@:2.8")
+
+    # Cargo
+    depends_on("openssl")
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix,
+                  '--llvm-root=' + spec['llvm'].prefix)
+
+        make()
+        make("install")
+
+        # Install cargo, rust package manager
+        with working_dir(os.path.join('cargo', 'cargo')):
+            get_submodules()
+            configure('--prefix=' + prefix,
+                      '--local-rust-root=' + prefix)
+
+            make()
+            make("install")
+
+    def setup_dependent_package(self, module, ext_spec):
+        """
+        Called before python modules' install() methods.
+
+        In most cases, extensions will only need to have one or two lines::
+
+            cargo('build')
+            cargo('install', '--root', prefix)
+
+        or
+
+            cargo('install', '--root', prefix)
+        """
+        # Rust extension builds can have a global cargo executable function
+        module.cargo = Executable(join_path(self.spec.prefix.bin, 'cargo'))
diff --git a/var/spack/repos/builtin/packages/scotch/Makefile.esmumps b/var/spack/repos/builtin/packages/scotch/Makefile.esmumps
deleted file mode 100644
index 4bfc760197..0000000000
--- a/var/spack/repos/builtin/packages/scotch/Makefile.esmumps
+++ /dev/null
@@ -1,5 +0,0 @@
-esmumps				:	scotch
-					(cd esmumps ; $(MAKE) scotch && $(MAKE) install)
-
-ptesmumps			:	ptscotch
-					(cd esmumps ; $(MAKE) ptscotch && $(MAKE) ptinstall)
diff --git a/var/spack/repos/builtin/packages/scotch/package.py b/var/spack/repos/builtin/packages/scotch/package.py
index 3abbf3c665..3c2b4993ac 100644
--- a/var/spack/repos/builtin/packages/scotch/package.py
+++ b/var/spack/repos/builtin/packages/scotch/package.py
@@ -23,7 +23,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-import re
 from spack import *
 
 
@@ -32,7 +31,7 @@ class Scotch(Package):
        partitioning, graph clustering, and sparse matrix ordering."""
 
     homepage = "http://www.labri.fr/perso/pelegrin/scotch/"
-    url      = "http://gforge.inria.fr/frs/download.php/latestfile/298/scotch_6.0.3.tar.gz"
+    url = "http://gforge.inria.fr/frs/download.php/latestfile/298/scotch_6.0.3.tar.gz"
     base_url = "http://gforge.inria.fr/frs/download.php/latestfile/298"
     list_url = "http://gforge.inria.fr/frs/?group_id=248"
 
@@ -44,6 +43,7 @@ class Scotch(Package):
     variant('compression', default=True, description='Activate the posibility to use compressed files')
     variant('esmumps', default=False, description='Activate the compilation of esmumps needed by mumps')
     variant('shared', default=True, description='Build a shared version of the library')
+    variant('metis', default=True, description='Build metis and parmetis wrapper libraries')
 
     depends_on('flex')
     depends_on('bison')
@@ -56,37 +56,15 @@ class Scotch(Package):
     # from the Scotch hosting site.  These alternative archives include a
     # superset of the behavior in their default counterparts, so we choose to
     # always grab these versions for older Scotch versions for simplicity.
-    @when('@:6.0.0')
-    def url_for_version(self, version):
-        return '%s/scotch_%s_esmumps.tar.gz' % (Scotch.base_url, version)
-
-    @when('@6.0.1:')
     def url_for_version(self, version):
         return super(Scotch, self).url_for_version(version)
 
-    # NOTE: Several of the 'esmumps' enabled Scotch releases up to version
-    # 6.0.0 have broken build scripts that don't properly build 'esmumps' as a
-    # separate target, so we need a patch procedure to remove 'esmumps' from
-    # existing targets and to add it as a standalone target.
     @when('@:6.0.0')
-    def patch(self):
-        makefile_path = os.path.join('src', 'Makefile')
-        with open(makefile_path, 'r') as makefile:
-            esmumps_enabled = any(re.search(r'^esmumps(\s*):(.*)$', line)
-                                  for line in makefile.readlines())
-
-        if not esmumps_enabled:
-            mff = FileFilter(makefile_path)
-            mff.filter(r'^.*((esmumps)|(ptesmumps)).*(install).*$', '')
-
-            mfesmumps_dir = os.path.dirname(os.path.realpath(__file__))
-            mfesmumps_path = os.path.join(mfesmumps_dir, 'Makefile.esmumps')
-            with open(makefile_path, 'a') as makefile:
-                makefile.write('\ninclude %s\n' % mfesmumps_path)
+    def url_for_version(self, version):
+        return '%s/scotch_%s_esmumps.tar.gz' % (Scotch.base_url, version)
 
-    @when('@6.0.1:')
     def patch(self):
-        pass
+        self.configure()
 
     # NOTE: Configuration of Scotch is achieved by writing a 'Makefile.inc'
     # file that contains all of the configuration variables and their desired
@@ -103,13 +81,13 @@ class Scotch(Package):
         ]
 
         # Library Build Type #
-
         if '+shared' in self.spec:
             makefile_inc.extend([
+                # todo change for Darwin systems
                 'LIB       = .so',
                 'CLIBFLAGS = -shared -fPIC',
                 'RANLIB    = echo',
-                'AR	       = $(CC)',
+                'AR        = $(CC)',
                 'ARFLAGS   = -shared $(LDFLAGS) -o'
             ])
             cflags.append('-fPIC')
@@ -118,7 +96,7 @@ class Scotch(Package):
                 'LIB       = .a',
                 'CLIBFLAGS = ',
                 'RANLIB    = ranlib',
-                'AR	       = ar',
+                'AR        = ar',
                 'ARFLAGS   = -ruv '
             ])
 
@@ -171,20 +149,49 @@ class Scotch(Package):
                 fh.write('\n'.join(makefile_inc))
 
     def install(self, spec, prefix):
-        self.configure()
-
         targets = ['scotch']
         if '+mpi' in self.spec:
             targets.append('ptscotch')
 
-        if '+esmumps' in self.spec:
-            targets.append('esmumps')
-            if '+mpi' in self.spec:
-                targets.append('ptesmumps')
+        if self.spec.version >= Version('6.0.0'):
+            if '+esmumps' in self.spec:
+                targets.append('esmumps')
+                if '+mpi' in self.spec:
+                    targets.append('ptesmumps')
 
         with working_dir('src'):
             for target in targets:
-                make(target, parallel=(target != 'ptesmumps'))
+                # It seams that building ptesmumps in parallel fails, for
+                # version prior to 6.0.0 there is no separated targets force
+                # ptesmumps, this library is built by the ptscotch target. This
+                # should explain the test for the can_make_parallel variable
+                can_make_parallel = \
+                    not (target == 'ptesmumps' or
+                         (self.spec.version < Version('6.0.0') and
+                          target == 'ptscotch'))
+                make(target, parallel=can_make_parallel)
+
+        # todo change this to take into account darwin systems
+        lib_ext = '.so' if '+shared' in self.spec else '.a'
+        # It seams easier to remove metis wrappers from the folder that will be
+        # installed than to tweak the Makefiles
+        if '+metis' not in self.spec:
+            with working_dir('lib'):
+                lib_ext = '.so' if '+shared' in self.spec else '.a'
+                force_remove('libscotchmetis{0}'.format(lib_ext))
+                force_remove('libptscotchparmetis{0}'.format(lib_ext))
+
+            with working_dir('include'):
+                force_remove('metis.h')
+                force_remove('parmetis.h')
+
+        if '~esmumps' in self.spec and self.spec.version < Version('6.0.0'):
+            with working_dir('lib'):
+                force_remove('libesmumps{0}'.format(lib_ext))
+                force_remove('libptesmumps{0}'.format(lib_ext))
+
+            with working_dir('include'):
+                force_remove('esmumps.h')
 
         install_tree('bin', prefix.bin)
         install_tree('lib', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/stream/package.py b/var/spack/repos/builtin/packages/stream/package.py
new file mode 100644
index 0000000000..8b3f32af8a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/stream/package.py
@@ -0,0 +1,62 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Stream(Package):
+    """The STREAM benchmark is a simple synthetic benchmark program that
+    measures sustainable memory bandwidth (in MB/s) and the corresponding
+    computation rate for simple vector kernels."""
+
+    homepage = "https://www.cs.virginia.edu/stream/ref.html"
+
+    version('5.10', git='https://github.com/jeffhammond/STREAM.git')
+
+    variant('openmp', default=False, description='Build with OpenMP support')
+
+    def patch(self):
+        makefile = FileFilter('Makefile')
+
+        # Use the Spack compiler wrappers
+        makefile.filter('CC = .*', 'CC = cc')
+        makefile.filter('FC = .*', 'FC = f77')
+
+        cflags = '-O2'
+        fflags = '-O2'
+        if '+openmp' in self.spec:
+            cflags += ' ' + self.compiler.openmp_flag
+            fflags += ' ' + self.compiler.openmp_flag
+
+        # Set the appropriate flags for this compiler
+        makefile.filter('CFLAGS = .*', 'CFLAGS = {0}'.format(cflags))
+        makefile.filter('FFLAGS = .*', 'FFLAGS = {0}'.format(fflags))
+
+    def install(self, spec, prefix):
+        make()
+
+        # Manual installation
+        mkdir(prefix.bin)
+        install('stream_c.exe', prefix.bin)
+        install('stream_f.exe', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/tbb/package.py b/var/spack/repos/builtin/packages/tbb/package.py
index 6c3ceb1e76..c88b170816 100644
--- a/var/spack/repos/builtin/packages/tbb/package.py
+++ b/var/spack/repos/builtin/packages/tbb/package.py
@@ -23,9 +23,9 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os
 import glob
 
+
 class Tbb(Package):
     """Widely used C++ template library for task parallelism.
     Intel Threading Building Blocks (Intel TBB) lets you easily write parallel
@@ -35,35 +35,39 @@ class Tbb(Package):
     homepage = "http://www.threadingbuildingblocks.org/"
 
     # Only version-specific URL's work for TBB
-    version('4.4.3', '80707e277f69d9b20eeebdd7a5f5331137868ce1', url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160128oss_src_0.tgz')
+    version('4.4.4', 'd4cee5e4ca75cab5181834877738619c56afeb71', url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160413oss_src.tgz')    # NOQA: ignore=E501
+    version('4.4.3', '80707e277f69d9b20eeebdd7a5f5331137868ce1', url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160128oss_src_0.tgz')  # NOQA: ignore=E501
 
-    def coerce_to_spack(self,tbb_build_subdir):
-        for compiler in ["icc","gcc","clang"]:
-              fs = glob.glob(join_path(tbb_build_subdir,"*.%s.inc" % compiler ))
-              for f in fs:
-                  lines = open(f).readlines()
-                  of = open(f,"w")
-                  for l in lines:
-                      if l.strip().startswith("CPLUS ="):
+    def coerce_to_spack(self, tbb_build_subdir):
+        for compiler in ["icc", "gcc", "clang"]:
+            fs = glob.glob(join_path(tbb_build_subdir,
+                                     "*.%s.inc" % compiler))
+            for f in fs:
+                lines = open(f).readlines()
+                of = open(f, "w")
+                for l in lines:
+                    if l.strip().startswith("CPLUS ="):
                         of.write("# coerced to spack\n")
                         of.write("CPLUS = $(CXX)\n")
-                      elif l.strip().startswith("CPLUS ="):
+                    elif l.strip().startswith("CPLUS ="):
                         of.write("# coerced to spack\n")
                         of.write("CONLY = $(CC)\n")
-                      else:
-                        of.write(l);
+                    else:
+                        of.write(l)
 
     def install(self, spec, prefix):
-        #
-        # we need to follow TBB's compiler selection logic to get the proper build + link flags
-        # but we still need to use spack's compiler wrappers
+        if spec.satisfies('%gcc@6.1:') and spec.satisfies('@:4.4.3'):
+            raise InstallError('Only TBB 4.4.4 and above build with GCC 6.1!')
+
+        # We need to follow TBB's compiler selection logic to get the proper
+        # build + link flags but we still need to use spack's compiler wrappers
         # to accomplish this, we do two things:
         #
-        # * Look at the spack spec to determine which compiler we should pass to tbb's Makefile
+        # * Look at the spack spec to determine which compiler we should pass
+        #   to tbb's Makefile;
         #
         # * patch tbb's build system to use the compiler wrappers (CC, CXX) for
-        #    icc, gcc, clang
-        #    (see coerce_to_spack())
+        #   icc, gcc, clang (see coerce_to_spack());
         #
         self.coerce_to_spack("build")
 
@@ -74,7 +78,6 @@ class Tbb(Package):
         else:
             tbb_compiler = "gcc"
 
-
         mkdirp(prefix)
         mkdirp(prefix.lib)
 
@@ -82,10 +85,10 @@ class Tbb(Package):
         # tbb does not have a configure script or make install target
         # we simply call make, and try to put the pieces together
         #
-        make("compiler=%s"  %(tbb_compiler))
+        make("compiler=%s"  % (tbb_compiler))
 
         # install headers to {prefix}/include
-        install_tree('include',prefix.include)
+        install_tree('include', prefix.include)
 
         # install libs to {prefix}/lib
         tbb_lib_names = ["libtbb",
@@ -94,10 +97,10 @@ class Tbb(Package):
 
         for lib_name in tbb_lib_names:
             # install release libs
-            fs = glob.glob(join_path("build","*release",lib_name + ".*"))
+            fs = glob.glob(join_path("build", "*release", lib_name + ".*"))
             for f in fs:
                 install(f, prefix.lib)
             # install debug libs if they exist
-            fs = glob.glob(join_path("build","*debug",lib_name + "_debug.*"))
+            fs = glob.glob(join_path("build", "*debug", lib_name + "_debug.*"))
             for f in fs:
                 install(f, prefix.lib)