merge from develop

.coveragerc

@@ -0,0 +1,34 @@
+# -*- conf -*-
+# .coveragerc to control coverage.py
+[run]
+branch = True
+source = lib
+omit =
+     lib/spack/spack/test/*
+     lib/spack/env/*
+     lib/spack/docs/*
+     lib/spack/external/*
+
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if False:
+    if __name__ == .__main__.:
+
+ignore_errors = True
+
+[html]
+directory = htmlcov

.flake8

@@ -0,0 +1,20 @@
+# -*- conf -*-
+# flake8 settings for Spack.
+#
+# Below we describe which flake8 checks Spack ignores and what the
+# rationale is.
+#
+# Let people line things up nicely:
+# - E221: multiple spaces before operator
+# - E241: multiple spaces after ‘,’
+#
+# Spack allows wildcard imports:
+# - F403: disable wildcard import
+#
+# These are required to get the package.py files to test clean.
+# - F821: undefined name (needed for cmake, configure, etc.)
+# - F999: name name be undefined or undefined from star imports.
+#
+[flake8]
+ignore = E221,E241,F403,F821,F999
+max-line-length = 79

.gitignore

@@ -9,3 +9,5 @@
 /share/spack/dotkit
 /share/spack/modules
 /TAGS
+/htmlcov
+.coverage

.travis.yml

@@ -6,21 +6,35 @@ python:
 # Use new Travis infrastructure (Docker can't sudo yet)
 sudo: false
 
-# No need to install any deps.
+# Install coveralls to obtain code coverage
-install: true
+install:
+  - "pip install coveralls"
+  - "pip install flake8"
 
 before_install:
   # Need this for the git tests to succeed.
   - git config --global user.email "spack@example.com"
   - git config --global user.name "Test User"
 
+  # Need this to be able to compute the list of changed files
+  - git fetch origin develop:develop
+
 script:
+  # Regular spack setup and tests
   - . share/spack/setup-env.sh
   - spack compilers
   - spack config get compilers
-  - spack test
   - spack install -v libdwarf
 
+  # Run unit tests with code coverage
+  - coverage run bin/spack test
+
+  # Run flake8 code style checks.
+  - share/spack/qa/run-flake8
+
+after_success:
+  - coveralls
+
 notifications:
   email:
     recipients:

LICENSE

@@ -1,56 +1,62 @@
-Copyright (c) 2013-2014, Lawrence Livermore National Security, LLC.
+########################################################################
+GNU LESSER GENERAL PUBLIC LICENSE (Lesser GPL)
+Version 2.1, February 1999
+########################################################################
+Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 Produced at the Lawrence Livermore National Laboratory.
 
 This file is part of Spack.
-Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 LLNL-CODE-647188
 
 For details, see https://github.com/llnl/spack
 
 This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License (as published by
+it under the terms of the GNU Lesser General Public License (as
-the Free Software Foundation) version 2.1 dated February 1999.
+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 General Public License for more details.
+conditions of the GNU Lesser General Public License for more details.
 
-You should have received a copy of the GNU Lesser General Public License
+You should have received a copy of the GNU Lesser General Public
-along with this program; if not, write to the Free Software Foundation,
+License along with this program; if not, write to the Free Software
-Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 
-OUR NOTICE AND TERMS AND CONDITIONS OF THE GNU GENERAL PUBLIC LICENSE
+########################################################################
+LLNL NOTICE AND TERMS AND CONDITIONS OF THE GNU LGPL
 
-Our Preamble Notice
+LLNL Preamble Notice
 
-A. This notice is required to be provided under our contract with the
+A. This notice is required to be provided under LLNL's contract with
-U.S. Department of Energy (DOE). This work was produced at the
+   the U.S. Department of Energy (DOE). This work was produced at the
-Lawrence Livermore National Laboratory under Contract
+   Lawrence Livermore National Laboratory under Contract
-No. DE-AC52-07NA27344 with the DOE.
+   No. DE-AC52-07NA27344 with the DOE.
 
 B. Neither the United States Government nor Lawrence Livermore
-National Security, LLC nor any of their employees, makes any warranty,
+   National Security, LLC nor any of their employees, makes any
-express or implied, or assumes any liability or responsibility for the
+   warranty, express or implied, or assumes any liability or
-accuracy, completeness, or usefulness of any information, apparatus,
+   responsibility for the accuracy, completeness, or usefulness of any
-product, or process disclosed, or represents that its use would not
+   information, apparatus, product, or process disclosed, or
-infringe privately-owned rights.
+   represents that its use would not infringe privately-owned rights.
 
 C. Also, reference herein to any specific commercial products,
-process, or services by trade name, trademark, manufacturer or
+   process, or services by trade name, trademark, manufacturer or
-otherwise does not necessarily constitute or imply its endorsement,
+   otherwise does not necessarily constitute or imply its endorsement,
-recommendation, or favoring by the United States Government or
+   recommendation, or favoring by the United States Government or
-Lawrence Livermore National Security, LLC. The views and opinions of
+   Lawrence Livermore National Security, LLC. The views and opinions
-authors expressed herein do not necessarily state or reflect those of
+   of authors expressed herein do not necessarily state or reflect
-the United States Government or Lawrence Livermore National Security,
+   those of the United States Government or Lawrence Livermore
-LLC, and shall not be used for advertising or product endorsement
+   National Security, LLC, and shall not be used for advertising or
-purposes.
+   product endorsement purposes.
 
 The precise terms and conditions for copying, distribution and
 modification follows.
 
-GNU Lesser GPL terms and Conditions for Copying, Distribution, and
+########################################################################
-Modification
+GNU LESSER GENERAL PUBLIC LICENSE
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
 
 0. This License Agreement applies to any software library or other
 program which contains a notice placed by the copyright holder or

README.md

@@ -1,7 +1,8 @@
 ![image](share/spack/logo/spack-logo-text-64.png "Spack")
 ============
 
-[![Build Status](https://travis-ci.org/LLNL/spack.png?branch=develop)](https://travis-ci.org/LLNL/spack)
+[![Build Status](https://travis-ci.org/LLNL/spack.svg?branch=develop)](https://travis-ci.org/LLNL/spack)
+[![Coverage Status](https://coveralls.io/repos/github/LLNL/spack/badge.svg?branch=develop)](https://coveralls.io/github/LLNL/spack?branch=develop)
 
 Spack is a package management tool designed to support multiple
 versions and configurations of software on a wide variety of platforms
@@ -62,6 +63,11 @@ a [pull request](https://help.github.com/articles/using-pull-requests/).
 When you send your request, make ``develop`` the destination branch on the
 [Spack repository](https://github.com/LLNL/spack).
 
+Your contribution will need to pass all the tests run by the `spack test`
+command, as well as the formatting checks in `share/spack/qa/run-flake8`.
+You should run both of these before submitting your pull request, to
+ensure that the online checks succeed.
+
 Spack is using a rough approximation of the [Git
 Flow](http://nvie.com/posts/a-successful-git-branching-model/)
 branching model.  The ``develop`` branch contains the latest

bin/sbang

@@ -1,4 +1,28 @@
 #!/bin/bash
+##############################################################################
+# 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
+##############################################################################
 #
 # `sbang`: Run scripts with long shebang lines.
 #

bin/spack

@@ -1,27 +1,27 @@
 #!/usr/bin/env python
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
 if not sys.version_info[:2] >= (2,6):
@@ -152,7 +152,7 @@ def main():
     command = spack.cmd.get_command(args.command)
     try:
         return_val = command(parser, args)
-    except SpackError, e:
+    except SpackError as e:
         e.die()
     except KeyboardInterrupt:
         sys.stderr.write('\n')

bin/spack-python

@@ -1,27 +1,27 @@
 #!/bin/sh
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 #
 # spack-python

etc/spack/modules.yaml

@@ -5,4 +5,25 @@
 # although users can override these settings in their ~/.spack/modules.yaml.
 # -------------------------------------------------------------------------
 modules:
-  enable: ['tcl', 'dotkit']
+  enable:
+    - tcl
+    - dotkit
+  prefix_inspections:
+    bin:
+      - PATH
+    man:
+      - MANPATH
+    lib:
+      - LIBRARY_PATH
+      - LD_LIBRARY_PATH
+    lib64:
+      - LIBRARY_PATH
+      - LD_LIBRARY_PATH
+    include:
+      - CPATH
+    lib/pkgconfig:
+      - PKGCONFIG
+    lib64/pkgconfig:
+      - PKGCONFIG
+    '':
+      - CMAKE_PREFIX_PATH

lib/spack/docs/basic_usage.rst

@@ -149,26 +149,46 @@ customize an installation in :ref:`sec-specs`.
 ``spack uninstall``
 ~~~~~~~~~~~~~~~~~~~~~
 
-To uninstall a package, type ``spack uninstall <package>``.  This will
+To uninstall a package, type ``spack uninstall <package>``.  This will ask the user for
-completely remove the directory in which the package was installed.
+confirmation, and in case will completely remove the directory in which the package was installed.
 
 .. code-block:: sh
 
    spack uninstall mpich
 
 If there are still installed packages that depend on the package to be
-uninstalled, spack will refuse to uninstall it. You can override this
+uninstalled, spack will refuse to uninstall it.
-behavior with ``spack uninstall -f <package>``, but you risk breaking
-other installed packages. In general, it is safer to remove dependent
-packages *before* removing their dependencies.
 
-A line like ``spack uninstall mpich`` may be ambiguous, if multiple
+To uninstall a package and every package that depends on it, you may give the
-``mpich`` configurations are installed.  For example, if both
+`--dependents` option.
+
+.. code-block:: sh
+
+   spack uninstall --dependents mpich
+
+will display a list of all the packages that depends on `mpich` and, upon confirmation,
+will uninstall them in the right order.
+
+A line like
+
+.. code-block:: sh
+
+   spack uninstall mpich
+
+may be ambiguous, if multiple ``mpich`` configurations are installed.  For example, if both
 ``mpich@3.0.2`` and ``mpich@3.1`` are installed, ``mpich`` could refer
 to either one. Because it cannot determine which one to uninstall,
-Spack will ask you to provide a version number to remove the
+Spack will ask you either to provide a version number to remove the
-ambiguity.  As an example, ``spack uninstall mpich@3.1`` is
+ambiguity or use the ``--all`` option to uninstall all of the matching packages.
-unambiguous in this scenario.
+
+You may force uninstall a package with the `--force` option
+
+.. code-block:: sh
+
+   spack uninstall --force mpich
+
+but you risk breaking other installed packages. In general, it is safer to remove dependent
+packages *before* removing their dependencies or use the `--dependents` option.
 
 
 Seeing installed packages
@@ -226,6 +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
@@ -352,25 +378,32 @@ how this is done is in :ref:`sec-specs`.
 ``spack compiler add``
 ~~~~~~~~~~~~~~~~~~~~~~~
 
+An alias for ``spack compiler find``.
+
+.. _spack-compiler-find:
+
+``spack compiler find``
+~~~~~~~~~~~~~~~~~~~~~~~
+
 If you do not see a compiler in this list, but you want to use it with
-Spack, you can simply run ``spack compiler add`` with the path to
+Spack, you can simply run ``spack compiler find`` with the path to
 where the compiler is installed.  For example::
 
-    $ spack compiler add /usr/local/tools/ic-13.0.079
+    $ spack compiler find /usr/local/tools/ic-13.0.079
     ==> Added 1 new compiler to /Users/gamblin2/.spack/compilers.yaml
         intel@13.0.079
 
-Or you can run ``spack compiler add`` with no arguments to force
+Or you can run ``spack compiler find`` with no arguments to force
 auto-detection.  This is useful if you do not know where compilers are
 installed, but you know that new compilers have been added to your
 ``PATH``.  For example, using dotkit, you might do this::
 
     $ module load gcc-4.9.0
-    $ spack compiler add
+    $ spack compiler find
     ==> Added 1 new compiler to /Users/gamblin2/.spack/compilers.yaml
         gcc@4.9.0
 
-This loads the environment module for gcc-4.9.0 to get it into the
+This loads the environment module for gcc-4.9.0 to add it to
 ``PATH``, and then it adds the compiler to Spack.
 
 .. _spack-compiler-info:
@@ -761,7 +794,7 @@ versions are now filtered out.
 
 .. _shell-support:
 
-Environment modules
+Integration with module systems
 -------------------------------
 
 .. note::
@@ -771,9 +804,50 @@ Environment modules
    interface and/or generated module names may change in future
    versions.
 
-Spack provides some limited integration with environment module
+Spack provides some integration with
-systems to make it easier to use the packages it provides.
+`Environment Modules <http://modules.sourceforge.net/>`_
+and `Dotkit <https://computing.llnl.gov/?set=jobs&page=dotkit>`_ to make
+it easier to use the packages it installed.
 
+
+
+Installing Environment Modules
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+In order to use Spack's generated environment modules, you must have
+installed the *Environment Modules* package.  On many Linux
+distributions, this can be installed from the vendor's repository:
+
+.. code-block:: sh
+
+    yum install environment-modules # (Fedora/RHEL/CentOS)
+    apt-get install environment-modules # (Ubuntu/Debian)
+
+If your Linux distribution does not have
+Environment Modules, you can get it with Spack:
+
+.. code-block:: sh
+
+    spack install environment-modules
+
+
+In this case to activate it automatically you need to add the following two
+lines to your ``.bashrc`` profile (or similar):
+
+.. code-block:: sh
+
+   MODULES_HOME=`spack location -i environment-modules`
+   source ${MODULES_HOME}/Modules/init/bash
+
+If you use a Unix shell other than ``bash``, modify the commands above
+accordingly and source the appropriate file in
+``${MODULES_HOME}/Modules/init/``.
+
+
+.. TODO : Add a similar section on how to install dotkit ?
+
+Spack and module systems
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 You can enable shell support by sourcing some files in the
 ``/share/spack`` directory.
 
@@ -781,7 +855,7 @@ For ``bash`` or ``ksh``, run:
 
 .. code-block:: sh
 
-   . $SPACK_ROOT/share/spack/setup-env.sh
+   . ${SPACK_ROOT}/share/spack/setup-env.sh
 
 For ``csh`` and ``tcsh`` run:
 
@@ -793,17 +867,19 @@ For ``csh`` and ``tcsh`` run:
 You can put the above code in your ``.bashrc`` or ``.cshrc``, and
 Spack's shell support will be available on the command line.
 
-When you install a package with Spack, it automatically generates an
+When you install a package with Spack, it automatically generates a module file
-environment module that lets you add the package to your environment.
+that lets you add the package to your environment.
 
-Currently, Spack supports the generation of `TCL Modules
+Currently, Spack supports the generation of `Environment Modules
 <http://wiki.tcl.tk/12999>`_ and `Dotkit
 <https://computing.llnl.gov/?set=jobs&page=dotkit>`_.  Generated
 module files for each of these systems can be found in these
 directories:
 
-  * ``$SPACK_ROOT/share/spack/modules``
+.. code-block:: sh
-  * ``$SPACK_ROOT/share/spack/dotkit``
+
+  ${SPACK_ROOT}/share/spack/modules
+  ${SPACK_ROOT}/share/spack/dotkit
 
 The directories are automatically added to your ``MODULEPATH`` and
 ``DK_NODE`` environment variables when you enable Spack's `shell
@@ -859,8 +935,7 @@ of installed packages.
 
 The names here should look familiar, they're the same ones from
 ``spack find``.  You *can* use the names here directly.  For example,
-you could type either of these commands to load the callpath module
+you could type either of these commands to load the callpath module:
-(assuming dotkit and modules are installed):
 
 .. code-block:: sh
 
@@ -875,7 +950,7 @@ easy to type.  Luckily, Spack has its own interface for using modules
 and dotkits.  You can use the same spec syntax you're used to:
 
   =========================  ==========================
-  Modules                    Dotkit
+  Environment Modules        Dotkit
   =========================  ==========================
   ``spack load <spec>``      ``spack use <spec>``
   ``spack unload <spec>``    ``spack unuse <spec>``
@@ -942,15 +1017,216 @@ used ``gcc``.  You could therefore just type:
 
 To identify just the one built with the Intel compiler.
 
+Module files generation and customization
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Regenerating Module files
+Environment Modules and Dotkit files are generated when packages are installed,
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
+and are placed in the following directories under the Spack root:
 
-Module and dotkit files are generated when packages are installed, and
+.. code-block:: sh
-are placed in the following directories under the Spack root:
 
-  * ``$SPACK_ROOT/share/spack/modules``
+  ${SPACK_ROOT}/share/spack/modules
-  * ``$SPACK_ROOT/share/spack/dotkit``
+  ${SPACK_ROOT}/share/spack/dotkit
+
+The content that gets written in each module file can be customized in two ways:
+
+  1. overriding part of the ``spack.Package`` API within a ``package.py``
+  2. writing dedicated configuration files
+
+Override ``Package`` API
+^^^^^^^^^^^^^^^^^^^^^^^^
+There are currently two methods in ``spack.Package`` that may affect the content
+of module files:
+
+.. code-block:: python
+
+  def setup_environment(self, spack_env, run_env):
+      """Set up the compile and runtime environments for a package."""
+      pass
+
+.. code-block:: python
+
+  def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+      """Set up the environment of packages that depend on this one"""
+      pass
+
+As briefly stated in the comments, the first method lets you customize the
+module file content for the package you are currently writing, the second
+allows for modifications to your dependees module file. In both cases one
+needs to fill ``run_env`` with the desired list of environment modifications.
+
+Example : ``builtin/packages/python/package.py``
+""""""""""""""""""""""""""""""""""""""""""""""""
+
+The ``python`` package that comes with the ``builtin`` Spack repository
+overrides ``setup_dependent_environment`` in the following way:
+
+.. code-block:: python
+
+  def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+        # ...
+        if extension_spec.package.extends(self.spec):
+            run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir))
+
+to insert the appropriate ``PYTHONPATH`` modifications in the module
+files of python packages.
+
+Configuration files
+^^^^^^^^^^^^^^^^^^^
+
+Another way of modifying the content of module files is writing a
+``modules.yaml`` configuration file. Following usual Spack conventions, this
+file can be placed either at *site* or *user* scope.
+
+The default site configuration reads:
+
+ .. literalinclude:: ../../../etc/spack/modules.yaml
+    :language: yaml
+
+It basically inspects the installation prefixes for the
+existence of a few folders and, if they exist, it prepends a path to a given
+list of environment variables.
+
+For each module system that can be enabled a finer configuration is possible:
+
+.. code-block:: yaml
+
+ modules:
+   tcl:
+     # contains environment modules specific customizations
+   dotkit:
+     # contains dotkit specific customizations
+
+The structure under the ``tcl`` and ``dotkit`` keys is almost equal, and will
+be showcased in the following by some examples.
+
+Select module files by spec constraints
+"""""""""""""""""""""""""""""""""""""""
+Using spec syntax it's possible to have different customizations for different
+groups of module files.
+
+Considering :
+
+.. code-block:: yaml
+
+ modules:
+   tcl:
+     all: # Default addition for every package
+       environment:
+         set:
+           BAR: 'bar'
+     ^openmpi:: # A double ':' overrides previous rules
+       environment:
+         set:
+           BAR: 'baz'
+     zlib:
+       environment:
+         prepend_path:
+           LD_LIBRARY_PATH: 'foo'
+     zlib%gcc@4.8:
+       environment:
+         unset:
+         - FOOBAR
+
+what will happen is that:
+
+ - every module file will set ``BAR=bar``
+ - unless the associated spec satisfies ``^openmpi`` in which case ``BAR=baz``
+ - any spec that satisfies ``zlib`` will additionally prepend ``foo`` to ``LD_LIBRARY_PATH``
+ - any spec that satisfies ``zlib%gcc@4.8`` will additionally unset ``FOOBAR``
+
+.. note::
+  Order does matter
+    The modifications associated with the ``all`` keyword are always evaluated
+    first, no matter where they appear in the configuration file. All the other
+    spec constraints are instead evaluated top to bottom.
+
+Filter modifications out of module files
+""""""""""""""""""""""""""""""""""""""""
+
+Modifications to certain environment variables in module files are generated by
+default. Suppose you would like to avoid having ``CPATH`` and ``LIBRARY_PATH``
+modified by your dotkit modules. Then :
+
+.. code-block:: yaml
+
+  modules:
+    dotkit:
+      all:
+        filter:
+          environment_blacklist: ['CPATH', 'LIBRARY_PATH']  # Exclude changes to any of these variables
+
+will generate dotkit module files that will not contain modifications to either
+``CPATH`` or ``LIBRARY_PATH`` and environment module files that instead will
+contain those modifications.
+
+Autoload dependencies
+"""""""""""""""""""""
+
+The following lines in ``modules.yaml``:
+
+.. code-block:: yaml
+
+  modules:
+    tcl:
+      all:
+        autoload: 'direct'
+
+will produce environment module files that will automatically load their direct
+dependencies.
+
+.. note::
+  Allowed values for ``autoload`` statements
+    Allowed values for ``autoload`` statements are either ``none``, ``direct``
+    or ``all``. In ``tcl`` configuration it is possible to use the option
+    ``prerequisites`` that accepts the same values and will add ``prereq``
+    statements instead of automatically loading other modules.
+
+Blacklist or whitelist the generation of specific module files
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Sometimes it is desirable not to generate module files, a common use case being
+not providing the users with software built using the system compiler.
+
+A configuration file like:
+
+.. code-block:: yaml
+
+  modules:
+    tcl:
+      whitelist: ['gcc', 'llvm']  # Whitelist will have precedence over blacklist
+      blacklist: ['%gcc@4.4.7']  # Assuming gcc@4.4.7 is the system compiler
+
+will skip module file generation for anything that satisfies ``%gcc@4.4.7``,
+with the exception of specs that satisfy ``gcc`` or ``llvm``.
+
+Customize the naming scheme and insert conflicts
+""""""""""""""""""""""""""""""""""""""""""""""""
+
+A configuration file like:
+
+.. code-block:: yaml
+
+  modules:
+    tcl:
+      naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
+      all:
+        conflict: ['{name}', 'intel/14.0.1']
+
+will create module files that will conflict with ``intel/14.0.1`` and with the
+base directory of the same module, effectively preventing the possibility to
+load two or more versions of the same software at the same time.
+
+.. note::
+  Tokens available for the naming scheme
+    currently only the tokens shown in the example are available to construct
+    the naming scheme
+
+.. note::
+  The ``conflict`` option is ``tcl`` specific
+
+Regenerating module files
+^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Sometimes you may need to regenerate the modules files.  For example,
 if newer, fancier module support is added to Spack at some later date,
@@ -960,7 +1236,7 @@ new features.
 .. _spack-module:
 
 ``spack module refresh``
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+""""""""""""""""""""""""
 
 Running ``spack module refresh`` will remove the
 ``share/spack/modules`` and ``share/spack/dotkit`` directories, then
@@ -1186,6 +1462,51 @@ several variants:
 
        spack deactivate -a python
 
+Filesystem requirements
+--------------------------
+
+Spack currently needs to be run from a filesystem that supports
+``flock`` locking semantics.  Nearly all local filesystems and recent
+versions of NFS support this, but parallel filesystems may be mounted
+without ``flock`` support enabled.  You can determine how your
+filesystems are mounted with ``mount -p``.  The output for a Lustre
+filesystem might look like this:
+
+.. code-block:: sh
+
+   $ mount -l | grep lscratch
+   pilsner-mds1-lnet0@o2ib100:/lsd on /p/lscratchd type lustre (rw,nosuid,noauto,_netdev,lazystatfs,flock)
+   porter-mds1-lnet0@o2ib100:/lse on /p/lscratche type lustre (rw,nosuid,noauto,_netdev,lazystatfs,flock)
+
+Note the ``flock`` option on both Lustre mounts.  If you do not see
+this or a similar option for your filesystem, you may need ot ask your
+system administrator to enable ``flock``.
+
+This issue typically manifests with the error below:
+
+.. code-block:: sh
+
+   $ ./spack find
+   Traceback (most recent call last):
+   File "./spack", line 176, in <module>
+     main()
+   File "./spack", line 154, in main
+     return_val = command(parser, args)
+   File "./spack/lib/spack/spack/cmd/find.py", line 170, in find
+     specs = set(spack.installed_db.query(**q_args))
+   File "./spack/lib/spack/spack/database.py", line 551, in query
+     with self.read_transaction():
+   File "./spack/lib/spack/spack/database.py", line 598, in __enter__
+     if self._enter() and self._acquire_fn:
+   File "./spack/lib/spack/spack/database.py", line 608, in _enter
+     return self._db.lock.acquire_read(self._timeout)
+   File "./spack/lib/spack/llnl/util/lock.py", line 103, in acquire_read
+     self._lock(fcntl.LOCK_SH, timeout)   # can raise LockError.
+   File "./spack/lib/spack/llnl/util/lock.py", line 64, in _lock
+     fcntl.lockf(self._fd, op | fcntl.LOCK_NB)
+   IOError: [Errno 38] Function not implemented
+
+A nicer error message is TBD in future versions of Spack.
 
 Getting Help
 -----------------------

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
@@ -123,8 +123,68 @@ 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:
 

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

lib/spack/docs/packaging_guide.rst

@@ -703,6 +703,127 @@ Fetching a revision
 Subversion branches are handled as part of the directory structure, so
 you can check out a branch or tag by changing the ``url``.
 
+
+.. _license:
+
+Licensed software
+------------------------------------------
+
+In order to install licensed software, Spack needs to know a few more
+details about a package. The following class attributes should be defined.
+
+``license_required``
+~~~~~~~~~~~~~~~~~~~~~
+
+Boolean. If set to ``True``, this software requires a license. If set to
+``False``, all of the following attributes will be ignored. Defaults to
+``False``.
+
+``license_comment``
+~~~~~~~~~~~~~~~~~~~~~
+
+String. Contains the symbol used by the license manager to denote a comment.
+Defaults to ``#``.
+
+``license_files``
+~~~~~~~~~~~~~~~~~~~~~
+
+List of strings. These are files that the software searches for when
+looking for a license. All file paths must be relative to the installation
+directory. More complex packages like Intel may require multiple
+licenses for individual components. Defaults to the empty list.
+
+``license_vars``
+~~~~~~~~~~~~~~~~~~~~~
+
+List of strings. Environment variables that can be set to tell the software
+where to look for a license if it is not in the usual location. Defaults
+to the empty list.
+
+``license_url``
+~~~~~~~~~~~~~~~~~~~~~
+
+String. A URL pointing to license setup instructions for the software.
+Defaults to the empty string.
+
+For example, let's take a look at the package for the PGI compilers.
+
+.. code-block:: python
+
+    # Licensing
+    license_required = True
+    license_comment  = '#'
+    license_files    = ['license.dat']
+    license_vars     = ['PGROUPD_LICENSE_FILE', 'LM_LICENSE_FILE']
+    license_url      = 'http://www.pgroup.com/doc/pgiinstall.pdf'
+
+As you can see, PGI requires a license. Its license manager, FlexNet, uses
+the ``#`` symbol to denote a comment. It expects the license file to be
+named ``license.dat`` and to be located directly in the installation prefix.
+If you would like the installation file to be located elsewhere, simply set
+``PGROUPD_LICENSE_FILE`` or ``LM_LICENSE_FILE`` after installation. For
+further instructions on installation and licensing, see the URL provided.
+
+Let's walk through a sample PGI installation to see exactly what Spack is
+and isn't capable of. Since PGI does not provide a download URL, it must
+be downloaded manually. It can either be added to a mirror or located in
+the current directory when ``spack install pgi`` is run. See :ref:`mirrors`
+for instructions on setting up a mirror.
+
+After running ``spack install pgi``, the first thing that will happen is
+Spack will create a global license file located at
+``$SPACK_ROOT/etc/spack/licenses/pgi/license.dat``. It will then open up the
+file using the editor set in ``$EDITOR``, or vi if unset. It will look like
+this:
+
+.. code-block::
+
+    # A license is required to use pgi.
+    #
+    # The recommended solution is to store your license key in this global
+    # license file. After installation, the following symlink(s) will be
+    # added to point to this file (relative to the installation prefix):
+    #
+    #   license.dat
+    #
+    # Alternatively, use one of the following environment variable(s):
+    #
+    #   PGROUPD_LICENSE_FILE
+    #   LM_LICENSE_FILE
+    #
+    # If you choose to store your license in a non-standard location, you may
+    # set one of these variable(s) to the full pathname to the license file, or
+    # port@host if you store your license keys on a dedicated license server.
+    # You will likely want to set this variable in a module file so that it
+    # gets loaded every time someone tries to use pgi.
+    #
+    # For further information on how to acquire a license, please refer to:
+    #
+    #   http://www.pgroup.com/doc/pgiinstall.pdf
+    #
+    # You may enter your license below.
+
+You can add your license directly to this file, or tell FlexNet to use a
+license stored on a separate license server. Here is an example that
+points to a license server called licman1:
+
+.. code-block::
+
+    SERVER licman1.mcs.anl.gov 00163eb7fba5 27200
+    USE_SERVER
+
+If your package requires the license to install, you can reference the
+location of this global license using ``self.global_license_file``.
+After installation, symlinks for all of the files given in
+``license_files`` will be created, pointing to this global license.
+If you install a different version or variant of the package, Spack
+will automatically detect and reuse the already existing global license.
+
+If the software you are trying to package doesn't rely on license files,
+Spack will print a warning message, letting the user know that they
+need to set an environment variable or pointing them to installation
+documentation.
+
 .. _patching:
 
 Patches
@@ -1527,8 +1648,8 @@ 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
+:ref:`configuration`.  Sites using Spack can customize them to match
-match the preferences of their own users.
+the preferences of their own users.
 
 .. _spack-spec:
 
@@ -1561,60 +1682,8 @@ 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
+See the `documentation in the config section <concretization-preferences_>`_
-versions, depends_on, and variants during concretization.
+for more details.
-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.
 
 .. _install-method:
 
@@ -1803,15 +1872,15 @@ Compile-time library search paths
   * ``-L$dep_prefix/lib``
   * ``-L$dep_prefix/lib64``
 Runtime library search paths (RPATHs)
-  * ``-Wl,-rpath,$dep_prefix/lib``
+  * ``$rpath_flag$dep_prefix/lib``
-  * ``-Wl,-rpath,$dep_prefix/lib64``
+  * ``$rpath_flag$dep_prefix/lib64``
 Include search paths
   * ``-I$dep_prefix/include``
 
 An example of this would be the ``libdwarf`` build, which has one
 dependency: ``libelf``.  Every call to ``cc`` in the ``libdwarf``
 build will have ``-I$LIBELF_PREFIX/include``,
-``-L$LIBELF_PREFIX/lib``, and ``-Wl,-rpath,$LIBELF_PREFIX/lib``
+``-L$LIBELF_PREFIX/lib``, and ``$rpath_flag$LIBELF_PREFIX/lib``
 inserted on the command line.  This is done transparently to the
 project's build system, which will just think it's using a system
 where ``libelf`` is readily available.  Because of this, you **do
@@ -1831,6 +1900,48 @@ successfully find ``libdwarf.h`` and ``libdwarf.so``, without the
 packager having to provide ``--with-libdwarf=/path/to/libdwarf`` on
 the command line.
 
+.. note::
+
+    For most compilers, ``$rpath_flag`` is ``-Wl,-rpath,``. However, NAG
+    passes its flags to GCC instead of passing them directly to the linker.
+    Therefore, its ``$rpath_flag`` is doubly wrapped: ``-Wl,-Wl,,-rpath,``.
+    ``$rpath_flag`` can be overriden on a compiler specific basis in
+    ``lib/spack/spack/compilers/$compiler.py``.
+
+Compiler flags
+~~~~~~~~~~~~~~
+In rare circumstances such as compiling and running small unit tests, a package
+developer may need to know what are the appropriate compiler flags to enable
+features like ``OpenMP``, ``c++11``, ``c++14`` and alike. To that end the
+compiler classes in ``spack`` implement the following _properties_ :
+``openmp_flag``, ``cxx11_flag``, ``cxx14_flag``, which can be accessed in a
+package by ``self.compiler.cxx11_flag`` and alike. Note that the implementation
+is such that if a given compiler version does not support this feature, an
+error will be produced. Therefore package developers can also use these properties
+to assert that a compiler supports the requested feature. This is handy when a
+package supports additional variants like
+
+.. code-block:: python
+
+   variant('openmp', default=True, description="Enable OpenMP support.")
+
+Message Parsing Interface (MPI)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+It is common for high performance computing software/packages to use ``MPI``.
+As a result of conretization, a given package can be built using different
+implementations of MPI such as ``Openmpi``, ``MPICH`` or ``IntelMPI``.
+In some scenarios to configure a package one have to provide it with appropriate MPI
+compiler wrappers such as ``mpicc``, ``mpic++``.
+However different implementations of ``MPI`` may have different names for those
+wrappers.  In order to make package's ``install()`` method indifferent to the
+choice ``MPI`` implementation, each package which implements ``MPI`` sets up
+``self.spec.mpicc``, ``self.spec.mpicxx``, ``self.spec.mpifc`` and ``self.spec.mpif77``
+to point to ``C``, ``C++``, ``Fortran 90`` and ``Fortran 77`` ``MPI`` wrappers.
+Package developers are advised to use these variables, for example ``self.spec['mpi'].mpicc``
+instead of hard-coding ``join_path(self.spec['mpi'].prefix.bin, 'mpicc')`` for
+the reasons outlined above.
+
+
 Forking ``install()``
 ~~~~~~~~~~~~~~~~~~~~~
 

lib/spack/env/cc

@@ -1,27 +1,27 @@
 #!/bin/bash
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 #
 # Spack compiler wrapper script.
@@ -38,19 +38,27 @@
 #      -Wl,-rpath   arguments for dependency /lib directories.
 #
 
-# This is the list of environment variables that need to be set before
+# This is an array of environment variables that need to be set before
 # the script runs. They are set by routines in spack.build_environment
 # as part of spack.package.Package.do_install().
-parameters="
+parameters=(
-SPACK_PREFIX
+    SPACK_PREFIX
-SPACK_ENV_PATH
+    SPACK_ENV_PATH
-SPACK_DEBUG_LOG_DIR
+    SPACK_DEBUG_LOG_DIR
-SPACK_COMPILER_SPEC
+    SPACK_COMPILER_SPEC
-SPACK_SHORT_SPEC"
+    SPACK_CC_RPATH_ARG
+    SPACK_CXX_RPATH_ARG
+    SPACK_F77_RPATH_ARG
+    SPACK_FC_RPATH_ARG
+    SPACK_SHORT_SPEC
+)
 
 # The compiler input variables are checked for sanity later:
 #   SPACK_CC, SPACK_CXX, SPACK_F77, SPACK_FC
-# Debug flag is optional; set to true for debug logging:
+# The default compiler flags are passed from these variables:
+#   SPACK_CFLAGS, SPACK_CXXFLAGS, SPACK_FCFLAGS, SPACK_FFLAGS,
+#   SPACK_LDFLAGS, SPACK_LDLIBS
+# Debug env var is optional; set to true for debug logging:
 #   SPACK_DEBUG
 # Test command is used to unit test the compiler script.
 #   SPACK_TEST_COMMAND
@@ -64,13 +72,12 @@ function die {
     exit 1
 }
 
-for param in $parameters; do
+for param in ${parameters[@]}; do
     if [[ -z ${!param} ]]; then
-        die "Spack compiler must be run from spack!  Input $param was missing!"
+        die "Spack compiler must be run from Spack! Input '$param' is missing."
     fi
 done
 
-#
 # Figure out the type of compiler, the language, and the mode so that
 # the compiler script knows what to do.
 #
@@ -78,63 +85,57 @@ done
 # 'command' is set based on the input command to $SPACK_[CC|CXX|F77|F90]
 #
 # 'mode' is set to one of:
+#    vcheck  version check
 #    cpp     preprocess
 #    cc      compile
 #    as      assemble
 #    ld      link
 #    ccld    compile & link
-#    vcheck  version check
-#
-# Depending on the mode, we may or may not add extra rpaths.
-# This variable controls whether they are added.
-add_rpaths=true
 
 command=$(basename "$0")
+comp="CC"
 case "$command" in
+    cpp)
+        mode=cpp
+        ;;
     cc|c89|c99|gcc|clang|icc|pgcc|xlc)
         command="$SPACK_CC"
         language="C"
+        comp="CC"
+        lang_flags=C
         ;;
     c++|CC|g++|clang++|icpc|pgc++|xlc++)
         command="$SPACK_CXX"
         language="C++"
+        comp="CXX"
+        lang_flags=CXX
         ;;
     f90|fc|f95|gfortran|ifort|pgfortran|xlf90|nagfor)
         command="$SPACK_FC"
         language="Fortran 90"
+        comp="FC"
+        lang_flags=F
         ;;
     f77|gfortran|ifort|pgfortran|xlf|nagfor)
         command="$SPACK_F77"
         language="Fortran 77"
-        ;;
+        comp="F77"
-    cpp)
+        lang_flags=F
-        mode=cpp
         ;;
     ld)
         mode=ld
-
-        # Darwin's linker has a -r argument that merges object files
-        # together. It doesn't work with -rpath.
-        if [[ $OSTYPE = darwin* ]]; then
-            for arg in "$@"; do
-                if [ "$arg" = -r ]; then
-                    add_rpaths=false
-                    break
-	            fi
-            done
-        fi
         ;;
     *)
         die "Unkown compiler: $command"
         ;;
 esac
 
-# If any of the arguments below is present then the mode is vcheck. In
+# If any of the arguments below are present, then the mode is vcheck.
-# vcheck mode nothing is added in terms of extra search paths or
+# In vcheck mode, nothing is added in terms of extra search paths or
-# libraries
+# libraries.
-if [ -z "$mode" ]; then
+if [[ -z $mode ]]; then
     for arg in "$@"; do
-        if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
+        if [[ $arg == -v || $arg == -V || $arg == --version || $arg == -dumpversion ]]; then
             mode=vcheck
             break
         fi
@@ -142,24 +143,27 @@ if [ -z "$mode" ]; then
 fi
 
 # Finish setting up the mode.
-if [ -z "$mode" ]; then
+if [[ -z $mode ]]; then
     mode=ccld
     for arg in "$@"; do
-        if [ "$arg" = -E ]; then
+        if [[ $arg == -E ]]; then
             mode=cpp
             break
-        elif [ "$arg" = -S ]; then
+        elif [[ $arg == -S ]]; then
             mode=as
             break
-        elif [ "$arg" = -c ]; then
+        elif [[ $arg == -c ]]; then
             mode=cc
             break
         fi
     done
 fi
 
+# Set up rpath variable according to language.
+eval rpath=\$SPACK_${comp}_RPATH_ARG
+
 # Dump the version and exit if we're in testing mode.
-if [ "$SPACK_TEST_COMMAND" = "dump-mode" ]; then
+if [[ $SPACK_TEST_COMMAND == dump-mode ]]; then
     echo "$mode"
     exit
 fi
@@ -170,30 +174,79 @@ if [[ -z $command ]]; then
     die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
 fi
 
-if [ "$mode" == vcheck ] ; then
+if [[ $mode == vcheck ]]; then
     exec ${command} "$@"
 fi
 
+# Darwin's linker has a -r argument that merges object files together.
+# It doesn't work with -rpath.
+# This variable controls whether they are added.
+add_rpaths=true
+if [[ $mode == ld && "$SPACK_SHORT_SPEC" =~ "darwin" ]]; then
+    for arg in "$@"; do
+        if [[ $arg == -r ]]; then
+            add_rpaths=false
+            break
+        fi
+    done
+fi
+
 # Save original command for debug logging
 input_command="$@"
 args=("$@")
 
+# Prepend cppflags, cflags, cxxflags, fcflags, fflags, and ldflags
+
+# Add ldflags
+case "$mode" in
+    ld|ccld)
+        args=(${SPACK_LDFLAGS[@]} "${args[@]}") ;;
+esac
+
+# Add compiler flags.
+case "$mode" in
+    cc|ccld)
+    # Add c, cxx, fc, and f flags
+        case $lang_flags in
+            C)
+                args=(${SPACK_CFLAGS[@]} "${args[@]}") ;;
+            CXX)
+                args=(${SPACK_CXXFLAGS[@]} "${args[@]}") ;;
+        esac
+        ;;
+esac
+
+# Add cppflags
+case "$mode" in
+    cpp|as|cc|ccld)
+        args=(${SPACK_CPPFLAGS[@]} "${args[@]}") ;;
+esac
+
+case "$mode" in cc|ccld)
+        # Add fortran flags
+        case $lang_flags in
+            F)
+                args=(${SPACK_FFLAGS[@]} "${args[@]}") ;;
+        esac
+        ;;
+esac
+
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
     # Prepend include directories
     if [[ -d $dep/include ]]; then
-        if [[ $mode = cpp || $mode = cc || $mode = as || $mode = ccld ]]; then
+        if [[ $mode == cpp || $mode == cc || $mode == as || $mode == ccld ]]; then
             args=("-I$dep/include" "${args[@]}")
         fi
     fi
 
     # Prepend lib and RPATH directories
     if [[ -d $dep/lib ]]; then
-        if [[ $mode = ccld ]]; then
+        if [[ $mode == ccld ]]; then
-            $add_rpaths && args=("-Wl,-rpath,$dep/lib" "${args[@]}")
+            $add_rpaths && args=("$rpath$dep/lib" "${args[@]}")
             args=("-L$dep/lib" "${args[@]}")
-        elif [[ $mode = ld ]]; then
+        elif [[ $mode == ld ]]; then
             $add_rpaths && args=("-rpath" "$dep/lib" "${args[@]}")
             args=("-L$dep/lib" "${args[@]}")
         fi
@@ -201,10 +254,10 @@ for dep in "${deps[@]}"; do
 
     # Prepend lib64 and RPATH directories
     if [[ -d $dep/lib64 ]]; then
-        if [[ $mode = ccld ]]; then
+        if [[ $mode == ccld ]]; then
-            $add_rpaths && args=("-Wl,-rpath,$dep/lib64" "${args[@]}")
+            $add_rpaths && args=("$rpath$dep/lib64" "${args[@]}")
             args=("-L$dep/lib64" "${args[@]}")
-        elif [[ $mode = ld ]]; then
+        elif [[ $mode == ld ]]; then
             $add_rpaths && args=("-rpath" "$dep/lib64" "${args[@]}")
             args=("-L$dep/lib64" "${args[@]}")
         fi
@@ -212,12 +265,20 @@ for dep in "${deps[@]}"; do
 done
 
 # Include all -L's and prefix/whatever dirs in rpath
-if [[ $mode = ccld ]]; then
+if [[ $mode == ccld ]]; then
-    $add_rpaths && args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
+    $add_rpaths && args=("$rpath$SPACK_PREFIX/lib64" "${args[@]}")
-elif [[ $mode = ld ]]; then
+    $add_rpaths && args=("$rpath$SPACK_PREFIX/lib"   "${args[@]}")
-    $add_rpaths && args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
+elif [[ $mode == ld ]]; then
+    $add_rpaths && args=("-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
+    $add_rpaths && args=("-rpath" "$SPACK_PREFIX/lib"   "${args[@]}")
 fi
 
+# Add SPACK_LDLIBS to args
+case "$mode" in
+    ld|ccld)
+        args=("${args[@]}" ${SPACK_LDLIBS[@]}) ;;
+esac
+
 #
 # Unset pesky environment variables that could affect build sanity.
 #
@@ -234,11 +295,14 @@ IFS=':' read -ra spack_env_dirs <<< "$SPACK_ENV_PATH"
 spack_env_dirs+=("" ".")
 PATH=""
 for dir in "${env_path[@]}"; do
-    remove=""
+    addpath=true
-    for rm_dir in "${spack_env_dirs[@]}"; do
+    for env_dir in "${spack_env_dirs[@]}"; do
-        if [[ $dir = $rm_dir ]]; then remove=True; fi
+        if [[ $dir == $env_dir ]]; then
+            addpath=false
+            break
+        fi
     done
-    if [[ -z $remove ]]; then
+    if $addpath; then
         PATH="${PATH:+$PATH:}$dir"
     fi
 done
@@ -247,7 +311,7 @@ export PATH
 full_command=("$command" "${args[@]}")
 
 # In test command mode, write out full command for Spack tests.
-if [[ $SPACK_TEST_COMMAND = dump-args ]]; then
+if [[ $SPACK_TEST_COMMAND == dump-args ]]; then
     echo "${full_command[@]}"
     exit
 elif [[ -n $SPACK_TEST_COMMAND ]]; then
@@ -257,7 +321,7 @@ fi
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
-if [[ $SPACK_DEBUG = TRUE ]]; then
+if [[ $SPACK_DEBUG == TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
     echo "[$mode] $command $input_command" >> $input_log

lib/spack/external/nose/LICENSE

@@ -55,7 +55,7 @@ modified by someone else and passed on, the recipients should know
 that what they have is not the original version, so that the original
 author's reputation will not be affected by problems that might be
 introduced by others.
-
+
   Finally, software patents pose a constant threat to the existence of
 any free program.  We wish to make sure that a company cannot
 effectively restrict the users of a free program by obtaining a
@@ -111,7 +111,7 @@ modification follow.  Pay close attention to the difference between a
 "work based on the library" and a "work that uses the library".  The
 former contains code derived from the library, whereas the latter must
 be combined with the library in order to run.
-
+
 		  GNU LESSER GENERAL PUBLIC LICENSE
    TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
 
@@ -158,7 +158,7 @@ Library.
   You may charge a fee for the physical act of transferring a copy,
 and you may at your option offer warranty protection in exchange for a
 fee.
-
+
   2. You may modify your copy or copies of the Library or any portion
 of it, thus forming a work based on the Library, and copy and
 distribute such modifications or work under the terms of Section 1
@@ -216,7 +216,7 @@ instead of to this License.  (If a newer version than version 2 of the
 ordinary GNU General Public License has appeared, then you can specify
 that version instead if you wish.)  Do not make any other change in
 these notices.
-
+
   Once this change is made in a given copy, it is irreversible for
 that copy, so the ordinary GNU General Public License applies to all
 subsequent copies and derivative works made from that copy.
@@ -267,7 +267,7 @@ Library will still fall under Section 6.)
 distribute the object code for the work under the terms of Section 6.
 Any executables containing that work also fall under Section 6,
 whether or not they are linked directly with the Library itself.
-
+
   6. As an exception to the Sections above, you may also combine or
 link a "work that uses the Library" with the Library to produce a
 work containing portions of the Library, and distribute that work
@@ -329,7 +329,7 @@ restrictions of other proprietary libraries that do not normally
 accompany the operating system.  Such a contradiction means you cannot
 use both them and the Library together in an executable that you
 distribute.
-
+
   7. You may place library facilities that are a work based on the
 Library side-by-side in a single library together with other library
 facilities not covered by this License, and distribute such a combined
@@ -370,7 +370,7 @@ subject to these terms and conditions.  You may not impose any further
 restrictions on the recipients' exercise of the rights granted herein.
 You are not responsible for enforcing compliance by third parties with
 this License.
-
+
   11. If, as a consequence of a court judgment or allegation of patent
 infringement or for any other reason (not limited to patent issues),
 conditions are imposed on you (whether by court order, agreement or
@@ -422,7 +422,7 @@ conditions either of that version or of any later version published by
 the Free Software Foundation.  If the Library does not specify a
 license version number, you may choose any version ever published by
 the Free Software Foundation.
-
+
   14. If you wish to incorporate parts of the Library into other free
 programs whose distribution conditions are incompatible with these,
 write to the author to ask for permission.  For software which is
@@ -456,7 +456,7 @@ SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
 DAMAGES.
 
 		     END OF TERMS AND CONDITIONS
-
+
            How to Apply These Terms to Your New Libraries
 
   If you develop a new library, and you want it to be of the greatest
@@ -500,5 +500,3 @@ necessary.  Here is a sample; alter the names:
   Ty Coon, President of Vice
 
 That's all there is to it!
-
-

lib/spack/llnl/__init__.py

@@ -0,0 +1,24 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################

lib/spack/llnl/util/__init__.py

@@ -0,0 +1,24 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################

lib/spack/llnl/util/filesystem.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 __all__ = ['set_install_permissions', 'install', 'install_tree', 'traverse_tree',
            'expand_user', 'working_dir', 'touch', 'touchp', 'mkdirp',

lib/spack/llnl/util/lang.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import re

lib/spack/llnl/util/link_tree.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """LinkTree class for setting up trees of symbolic links."""
 __all__ = ['LinkTree']

lib/spack/llnl/util/lock.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import fcntl

lib/spack/llnl/util/tty/__init__.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
 import os

lib/spack/llnl/util/tty/colify.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 Routines for printing columnar output.  See colify() for more information.

lib/spack/llnl/util/tty/color.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 This file implements an expression syntax, similar to printf, for adding

lib/spack/llnl/util/tty/log.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """Utility classes for logging the output of blocks of code.
 """

lib/spack/spack/__init__.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import sys
@@ -109,7 +109,7 @@
 
 # Version information
 from spack.version import Version
-spack_version = Version("0.8.15")
+spack_version = Version("0.9")
 
 #
 # Executables used by Spack
@@ -140,9 +140,7 @@
     # don't add a second username if it's already unique by user.
     if not _tmp_user in path:
         tmp_dirs.append(join_path(path, '%u', 'spack-stage'))
-
+    else:
-for path in _tmp_candidates:
-    if not path in tmp_dirs:
         tmp_dirs.append(join_path(path, 'spack-stage'))
 
 # Whether spack should allow installation of unsafe versions of

lib/spack/spack/abi.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://scalability-llnl.github.io/spack
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 
 import os

lib/spack/spack/architecture.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import re
@@ -34,14 +34,14 @@
 
 class InvalidSysTypeError(serr.SpackError):
     def __init__(self, sys_type):
-        super(InvalidSysTypeError, self).__init__(
+        super(InvalidSysTypeError,
-            "Invalid sys_type value for Spack: " + sys_type)
+              self).__init__("Invalid sys_type value for Spack: " + sys_type)
 
 
 class NoSysTypeError(serr.SpackError):
     def __init__(self):
-        super(NoSysTypeError, self).__init__(
+        super(NoSysTypeError,
-            "Could not determine sys_type for this machine.")
+              self).__init__("Could not determine sys_type for this machine.")
 
 
 def get_sys_type_from_spack_globals():
@@ -69,15 +69,15 @@ def get_sys_type_from_platform():
 @memoized
 def sys_type():
     """Returns a SysType for the current machine."""
-    methods = [get_sys_type_from_spack_globals,
+    methods = [get_sys_type_from_spack_globals, get_sys_type_from_environment,
-               get_sys_type_from_environment,
                get_sys_type_from_platform]
 
     # search for a method that doesn't return None
     sys_type = None
     for method in methods:
         sys_type = method()
-        if sys_type: break
+        if sys_type:
+            break
 
     # Couldn't determine the sys_type for this machine.
     if sys_type is None:

lib/spack/spack/build_environment.py

@@ -1,3 +1,27 @@
+##############################################################################
+# 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
+##############################################################################
 """
 This module contains all routines related to setting up the package
 build environment.  All of this is set up by package.py just before
@@ -27,15 +51,16 @@
 Skimming this module is a nice way to get acquainted with the types of
 calls you can make from within the install() function.
 """
-import multiprocessing
 import os
-import platform
-import shutil
 import sys
+import shutil
+import multiprocessing
+import platform
 
-import spack
 import llnl.util.tty as tty
 from llnl.util.filesystem import *
+
+import spack
 from spack.environment import EnvironmentModifications, validate
 from spack.util.environment import *
 from spack.util.executable import Executable, which
@@ -91,20 +116,22 @@ def __call__(self, *args, **kwargs):
 
 def set_compiler_environment_variables(pkg, env):
     assert pkg.spec.concrete
+    compiler = pkg.compiler
+    flags = pkg.spec.compiler_flags
+
     # Set compiler variables used by CMake and autotools
-    assert all(key in pkg.compiler.link_paths for key in ('cc', 'cxx', 'f77', 'fc'))
+    assert all(key in compiler.link_paths for key in ('cc', 'cxx', 'f77', 'fc'))
 
     # Populate an object with the list of environment modifications
     # and return it
     # TODO : add additional kwargs for better diagnostics, like requestor, ttyout, ttyerr, etc.
     link_dir = spack.build_env_path
-    env.set('CC', join_path(link_dir, pkg.compiler.link_paths['cc']))
+    env.set('CC',  join_path(link_dir, compiler.link_paths['cc']))
-    env.set('CXX', join_path(link_dir, pkg.compiler.link_paths['cxx']))
+    env.set('CXX', join_path(link_dir, compiler.link_paths['cxx']))
-    env.set('F77', join_path(link_dir, pkg.compiler.link_paths['f77']))
+    env.set('F77', join_path(link_dir, compiler.link_paths['f77']))
-    env.set('FC', join_path(link_dir, pkg.compiler.link_paths['fc']))
+    env.set('FC',  join_path(link_dir, compiler.link_paths['fc']))
 
     # Set SPACK compiler variables so that our wrapper knows what to call
-    compiler = pkg.compiler
     if compiler.cc:
         env.set('SPACK_CC', compiler.cc)
     if compiler.cxx:
@@ -114,6 +141,18 @@ def set_compiler_environment_variables(pkg, env):
     if compiler.fc:
         env.set('SPACK_FC',  compiler.fc)
 
+    # Set SPACK compiler rpath flags so that our wrapper knows what to use
+    env.set('SPACK_CC_RPATH_ARG',  compiler.cc_rpath_arg)
+    env.set('SPACK_CXX_RPATH_ARG', compiler.cxx_rpath_arg)
+    env.set('SPACK_F77_RPATH_ARG', compiler.f77_rpath_arg)
+    env.set('SPACK_FC_RPATH_ARG',  compiler.fc_rpath_arg)
+
+    # Add every valid compiler flag to the environment, prefixed with "SPACK_"
+    for flag in spack.spec.FlagMap.valid_compiler_flags():
+        # Concreteness guarantees key safety here
+        if flags[flag] != []:
+            env.set('SPACK_' + flag.upper(), ' '.join(f for f in flags[flag]))
+
     env.set('SPACK_COMPILER_SPEC', str(pkg.spec.compiler))
     return env
 
@@ -175,8 +214,8 @@ def set_build_environment_variables(pkg, env):
     # Add any pkgconfig directories to PKG_CONFIG_PATH
     pkg_config_dirs = []
     for p in dep_prefixes:
-        for libdir in ('lib', 'lib64'):
+        for maybe in ('lib', 'lib64', 'share'):
-            pcdir = join_path(p, libdir, 'pkgconfig')
+            pcdir = join_path(p, maybe, 'pkgconfig')
             if os.path.isdir(pcdir):
                 pkg_config_dirs.append(pcdir)
     env.set_path('PKG_CONFIG_PATH', pkg_config_dirs)
@@ -213,7 +252,7 @@ def set_module_variables_for_package(pkg, module):
     # TODO: of build dependencies, as opposed to link dependencies.
     # TODO: Currently, everything is a link dependency, but tools like
     # TODO: this shouldn't be.
-    m.cmake = which("cmake")
+    m.cmake = Executable('cmake')
 
     # standard CMake arguments
     m.std_cmake_args = ['-DCMAKE_INSTALL_PREFIX=%s' % pkg.prefix,
@@ -278,21 +317,6 @@ def parent_class_modules(cls):
     return result
 
 
-def setup_module_variables_for_dag(pkg):
-    """Set module-scope variables for all packages in the DAG."""
-    for spec in pkg.spec.traverse(order='post'):
-        # If a user makes their own package repo, e.g.
-        # spack.repos.mystuff.libelf.Libelf, and they inherit from
-        # an existing class like spack.repos.original.libelf.Libelf,
-        # then set the module variables for both classes so the
-        # parent class can still use them if it gets called.
-        spkg = spec.package
-        modules = parent_class_modules(spkg.__class__)
-        for mod in modules:
-            set_module_variables_for_package(spkg, mod)
-        set_module_variables_for_package(spkg, spkg.module)
-
-
 def setup_package(pkg):
     """Execute all environment setup routines."""
     spack_env = EnvironmentModifications()
@@ -316,20 +340,27 @@ def setup_package(pkg):
 
     set_compiler_environment_variables(pkg, spack_env)
     set_build_environment_variables(pkg, spack_env)
-    setup_module_variables_for_dag(pkg)
+
+    # traverse in postorder so package can use vars from its dependencies
+    spec = pkg.spec
+    for dspec in pkg.spec.traverse(order='post', root=False):
+        # If a user makes their own package repo, e.g.
+        # spack.repos.mystuff.libelf.Libelf, and they inherit from
+        # an existing class like spack.repos.original.libelf.Libelf,
+        # then set the module variables for both classes so the
+        # parent class can still use them if it gets called.
+        spkg = dspec.package
+        modules = parent_class_modules(spkg.__class__)
+        for mod in modules:
+            set_module_variables_for_package(spkg, mod)
+        set_module_variables_for_package(spkg, spkg.module)
 
         # Allow dependencies to modify the module
-    spec = pkg.spec
+        dpkg = dspec.package
-    for dependency_spec in spec.traverse(root=False):
-        dpkg = dependency_spec.package
         dpkg.setup_dependent_package(pkg.module, spec)
-
-    # Allow dependencies to set up environment as well
-    for dependency_spec in spec.traverse(root=False):
-        dpkg = dependency_spec.package
         dpkg.setup_dependent_environment(spack_env, run_env, spec)
 
-    # Allow the package to apply some settings.
+    set_module_variables_for_package(pkg, pkg.module)
     pkg.setup_environment(spack_env, run_env)
 
     # Make sure nothing's strange about the Spack environment.

lib/spack/spack/cmd/__init__.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import re

lib/spack/spack/cmd/activate.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import llnl.util.tty as tty

lib/spack/spack/cmd/arch.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import spack
 import spack.architecture as architecture

lib/spack/spack/cmd/bootstrap.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 from subprocess import check_call

lib/spack/spack/cmd/cd.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import spack.cmd.location
 import spack.modules

lib/spack/spack/cmd/checksum.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import hashlib

lib/spack/spack/cmd/clean.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2014, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 

lib/spack/spack/cmd/compiler.py

@@ -1,40 +1,39 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import sys
 import argparse
+import sys
 
 import llnl.util.tty as tty
-from llnl.util.tty.color import colorize
-from llnl.util.tty.colify import colify
-from llnl.util.lang import index_by
-
 import spack.compilers
-import spack.spec
 import spack.config
-from spack.util.environment import get_path
+import spack.spec
+from llnl.util.lang import index_by
+from llnl.util.tty.colify import colify
+from llnl.util.tty.color import colorize
 from spack.spec import CompilerSpec
+from spack.util.environment import get_path
 
 description = "Manage compilers"
 
@@ -44,10 +43,10 @@ def setup_parser(subparser):
 
     scopes = spack.config.config_scopes
 
-    # Add
+    # Find
-    add_parser = sp.add_parser('add', help='Add compilers to the Spack configuration.')
+    find_parser = sp.add_parser('find', aliases=['add'], help='Search the system for compilers to add to the Spack configuration.')
-    add_parser.add_argument('add_paths', nargs=argparse.REMAINDER)
+    find_parser.add_argument('add_paths', nargs=argparse.REMAINDER)
-    add_parser.add_argument('--scope', choices=scopes, default=spack.cmd.default_modify_scope,
+    find_parser.add_argument('--scope', choices=scopes, default=spack.cmd.default_modify_scope,
                             help="Configuration scope to modify.")
 
     # Remove
@@ -70,7 +69,7 @@ def setup_parser(subparser):
                              help="Configuration scope to read from.")
 
 
-def compiler_add(args):
+def compiler_find(args):
     """Search either $PATH or a list of paths for compilers and add them
        to Spack's configuration."""
     paths = args.add_paths
@@ -136,7 +135,8 @@ def compiler_list(args):
 
 
 def compiler(parser, args):
-    action = { 'add'    : compiler_add,
+    action = { 'add'    : compiler_find,
+               'find'   : compiler_find,
                'remove' : compiler_remove,
                'rm'     : compiler_remove,
                'info'   : compiler_info,

lib/spack/spack/cmd/compilers.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import llnl.util.tty as tty
 from llnl.util.tty.colify import colify

lib/spack/spack/cmd/config.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
 import argparse

lib/spack/spack/cmd/create.py

@@ -1,27 +1,29 @@
+_copyright = """\
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
+"""
 import string
 import os
 import hashlib
@@ -47,22 +49,22 @@
 
 description = "Create a new package file from an archive URL"
 
-package_template = string.Template("""\
+package_template = string.Template(
-# FIXME:
+    _copyright + """
-# This is a template package file for Spack.  We've conveniently
-# put "FIXME" labels next to all the things you'll want to change.
 #
-# Once you've edited all the FIXME's, delete this whole message,
+# This is a template package file for Spack.  We've put "FIXME"
-# save this file, and test out your package like this:
+# next to all the things you'll want to change. Once you've handled
+# them, you can save this file and test your package like this:
 #
 #     spack install ${name}
 #
-# You can always get back here to change things with:
+# You can edit this file again by typing:
 #
 #     spack edit ${name}
 #
-# See the spack documentation for more information on building
+# See the Spack documentation for more information on packaging.
-# packages.
+# If you submit this package back to Spack as a pull request,
+# please first remove this boilerplate and all FIXME comments.
 #
 from spack import *
 
@@ -124,10 +126,12 @@ def __call__(self, stage):
         autotools = "configure('--prefix=%s' % prefix)"
         cmake     = "cmake('.', *std_cmake_args)"
         python    = "python('setup.py', 'install', '--prefix=%s' % prefix)"
+        r         = "R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)"
 
         config_lines = ((r'/configure$',      'autotools', autotools),
                         (r'/CMakeLists.txt$', 'cmake',     cmake),
-                        (r'/setup.py$',       'python',    python))
+                        (r'/setup.py$',       'python',    python),
+                        (r'/NAMESPACE$',      'r',         r))
 
         # Peek inside the tarball.
         tar = which('tar')
@@ -272,6 +276,10 @@ def create(parser, args):
     if guesser.build_system == 'python':
         name = 'py-%s' % name
 
+    # Prepend 'r-' to R package names, by convention.
+    if guesser.build_system == 'r':
+        name = 'r-%s' % name
+
     # Create a directory for the new package.
     pkg_path = repo.filename_for_package_name(name)
     if os.path.exists(pkg_path) and not args.force:

lib/spack/spack/cmd/deactivate.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import llnl.util.tty as tty

lib/spack/spack/cmd/dependents.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 

lib/spack/spack/cmd/diy.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
 import os

lib/spack/spack/cmd/doc.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 
 description = "Run pydoc from within spack."

lib/spack/spack/cmd/edit.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import string

lib/spack/spack/cmd/env.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import argparse

lib/spack/spack/cmd/extensions.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
 import argparse

lib/spack/spack/cmd/fetch.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 

lib/spack/spack/cmd/find.py

@@ -1,77 +1,100 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import sys
-import collections
-import itertools
 import argparse
-from StringIO import StringIO
+import sys
 
 import llnl.util.tty as tty
-from llnl.util.tty.colify import *
-from llnl.util.tty.color import *
-from llnl.util.lang import *
-
 import spack
 import spack.spec
+from llnl.util.lang import *
+from llnl.util.tty.colify import *
+from llnl.util.tty.color import *
+
+description = "Find installed spack packages"
 
-description ="Find installed spack packages"
 
 def setup_parser(subparser):
     format_group = subparser.add_mutually_exclusive_group()
-    format_group.add_argument(
+    format_group.add_argument('-s', '--short',
-        '-s', '--short', action='store_const', dest='mode', const='short',
+                              action='store_const',
+                              dest='mode',
+                              const='short',
                               help='Show only specs (default)')
-    format_group.add_argument(
+    format_group.add_argument('-p', '--paths',
-        '-p', '--paths', action='store_const', dest='mode', const='paths',
+                              action='store_const',
+                              dest='mode',
+                              const='paths',
                               help='Show paths to package install directories')
     format_group.add_argument(
-        '-d', '--deps', action='store_const', dest='mode', const='deps',
+        '-d', '--deps',
+        action='store_const',
+        dest='mode',
+        const='deps',
         help='Show full dependency DAG of installed packages')
 
-    subparser.add_argument(
+    subparser.add_argument('-l', '--long',
-        '-l', '--long', action='store_true',
+                           action='store_true',
+                           dest='long',
                            help='Show dependency hashes as well as versions.')
-    subparser.add_argument(
+    subparser.add_argument('-L', '--very-long',
-        '-L', '--very-long', action='store_true',
+                           action='store_true',
+                           dest='very_long',
                            help='Show dependency hashes as well as versions.')
+    subparser.add_argument('-f', '--show-flags',
+                           action='store_true',
+                           dest='show_flags',
+                           help='Show spec compiler flags.')
 
     subparser.add_argument(
-        '-u', '--unknown', action='store_true',
+        '-e', '--explicit',
+        action='store_true',
+        help='Show only specs that were installed explicitly')
+    subparser.add_argument(
+        '-E', '--implicit',
+        action='store_true',
+        help='Show only specs that were installed as dependencies')
+    subparser.add_argument(
+        '-u', '--unknown',
+        action='store_true',
+        dest='unknown',
         help='Show only specs Spack does not have a package for.')
     subparser.add_argument(
-        '-m', '--missing', action='store_true',
+        '-m', '--missing',
+        action='store_true',
+        dest='missing',
         help='Show missing dependencies as well as installed specs.')
-    subparser.add_argument(
+    subparser.add_argument('-M', '--only-missing',
-        '-M', '--only-missing', action='store_true',
+                           action='store_true',
+                           dest='only_missing',
                            help='Show only missing dependencies.')
-    subparser.add_argument(
+    subparser.add_argument('-N', '--namespace',
-        '-N', '--namespace', action='store_true',
+                           action='store_true',
                            help='Show fully qualified package names.')
 
-    subparser.add_argument(
+    subparser.add_argument('query_specs',
-        'query_specs', nargs=argparse.REMAINDER,
+                           nargs=argparse.REMAINDER,
                            help='optional specs to filter results')
 
 
@@ -89,23 +112,29 @@ def display_specs(specs, **kwargs):
         hashes = True
         hlen = None
 
+    nfmt = '.' if namespace else '_'
+    format_string = '$%s$@$+' % nfmt
+    flags = kwargs.get('show_flags', False)
+    if flags:
+        format_string = '$%s$@$%%+$+' % nfmt
+
     # Make a dict with specs keyed by architecture and compiler.
     index = index_by(specs, ('architecture', 'compiler'))
 
     # Traverse the index and print out each package
     for i, (architecture, compiler) in enumerate(sorted(index)):
-        if i > 0: print
+        if i > 0:
+            print
 
-        header = "%s{%s} / %s{%s}" % (
+        header = "%s{%s} / %s{%s}" % (spack.spec.architecture_color,
-            spack.spec.architecture_color, architecture,
+                                      architecture, spack.spec.compiler_color,
-            spack.spec.compiler_color, compiler)
+                                      compiler)
         tty.hline(colorize(header), char='-')
 
-        specs = index[(architecture,compiler)]
+        specs = index[(architecture, compiler)]
         specs.sort()
 
-        nfmt = '.' if namespace else '_'
+        abbreviated = [s.format(format_string, color=True) for s in specs]
-        abbreviated = [s.format('$%s$@$+' % nfmt, color=True) for s in specs]
         if mode == 'paths':
             # Print one spec per line along with prefix path
             width = max(len(s) for s in abbreviated)
@@ -114,18 +143,21 @@ def display_specs(specs, **kwargs):
 
             for abbrv, spec in zip(abbreviated, specs):
                 if hashes:
-                    print gray_hash(spec, hlen),
+                    print(gray_hash(spec, hlen), )
-                print format % (abbrv, spec.prefix)
+                print(format % (abbrv, spec.prefix))
 
         elif mode == 'deps':
             for spec in specs:
-                print spec.tree(
+                print(spec.tree(
-                    format='$%s$@$+' % nfmt,
+                    format=format_string,
                     color=True,
                     indent=4,
-                    prefix=(lambda s: gray_hash(s, hlen)) if hashes else None)
+                    prefix=(lambda s: gray_hash(s, hlen)) if hashes else None))
 
         elif mode == 'short':
+            # Print columns of output if not printing flags
+            if not flags:
+
                 def fmt(s):
                     string = ""
                     if hashes:
@@ -133,19 +165,26 @@ def fmt(s):
                     string += s.format('$-%s$@$+' % nfmt, color=True)
 
                     return string
+
                 colify(fmt(s) for s in specs)
+            # Print one entry per line if including flags
+            else:
+                for spec in specs:
+                    # Print the hash if necessary
+                    hsh = gray_hash(spec, hlen) + ' ' if hashes else ''
+                    print(hsh + spec.format(format_string, color=True) + '\n')
 
         else:
             raise ValueError(
-                "Invalid mode for display_specs: %s. Must be one of (paths, deps, short)." % mode)
+                "Invalid mode for display_specs: %s. Must be one of (paths,"
-
+                "deps, short)." % mode)  # NOQA: ignore=E501
 
 
 def find(parser, args):
     # Filter out specs that don't exist.
     query_specs = spack.cmd.parse_specs(args.query_specs)
     query_specs, nonexisting = partition_list(
-        query_specs, lambda s: spack.repo.exists(s.name))
+        query_specs, lambda s: spack.repo.exists(s.name) or not s.name)
 
     if nonexisting:
         msg = "No such package%s: " % ('s' if len(nonexisting) > 1 else '')
@@ -163,13 +202,21 @@ def find(parser, args):
         installed = any
     if args.unknown:
         known = False
-    q_args = { 'installed' : installed, 'known' : known }
+
+    explicit = any
+    if args.explicit:
+        explicit = False
+    if args.implicit:
+        explicit = True
+
+    q_args = {'installed': installed, 'known': known, "explicit": explicit}
 
     # Get all the specs the user asked for
     if not query_specs:
         specs = set(spack.installed_db.query(**q_args))
     else:
-        results = [set(spack.installed_db.query(qs, **q_args)) for qs in query_specs]
+        results = [set(spack.installed_db.query(qs, **q_args))
+                   for qs in query_specs]
         specs = set.union(*results)
 
     if not args.mode:
@@ -177,7 +224,8 @@ def find(parser, args):
 
     if sys.stdout.isatty():
         tty.msg("%d installed packages." % len(specs))
-    display_specs(specs, mode=args.mode,
+    display_specs(specs,
+                  mode=args.mode,
                   long=args.long,
                   very_long=args.very_long,
-                  namespace=args.namespace)
+                  show_flags=args.show_flags)

lib/spack/spack/cmd/graph.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 

lib/spack/spack/cmd/help.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
 

lib/spack/spack/cmd/info.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import textwrap
 from llnl.util.tty.colify import *

lib/spack/spack/cmd/install.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 
@@ -78,4 +78,5 @@ def install(parser, args):
                 ignore_deps=args.ignore_deps,
                 make_jobs=args.jobs,
                 verbose=args.verbose,
-                fake=args.fake)
+                fake=args.fake,
+                explicit=True)

lib/spack/spack/cmd/list.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
 import llnl.util.tty as tty

lib/spack/spack/cmd/load.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by David Beckingsale, david@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import spack.modules

lib/spack/spack/cmd/location.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import sys

lib/spack/spack/cmd/md5.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2014, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import hashlib

lib/spack/spack/cmd/mirror.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import sys

lib/spack/spack/cmd/module.py

@@ -1,54 +1,52 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import sys
 import os
 import shutil
-import argparse
+import sys
 
 import llnl.util.tty as tty
-from llnl.util.lang import partition_list
-from llnl.util.filesystem import mkdirp
-
 import spack.cmd
+from llnl.util.filesystem import mkdirp
 from spack.modules import module_types
 from spack.util.string import *
 
-from spack.spec import Spec
+description = "Manipulate modules and dotkits."
-
-description ="Manipulate modules and dotkits."
 
 
 def setup_parser(subparser):
     sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='module_command')
 
-    refresh_parser = sp.add_parser('refresh', help='Regenerate all module files.')
+    sp.add_parser('refresh', help='Regenerate all module files.')
 
     find_parser = sp.add_parser('find', help='Find module files for packages.')
-    find_parser.add_argument(
+    find_parser.add_argument('module_type',
-        'module_type', help="Type of module to find file for. [" + '|'.join(module_types) + "]")
+                             help="Type of module to find file for. [" +
-    find_parser.add_argument('spec', nargs='+', help='spec to find a module file for.')
+                             '|'.join(module_types) + "]")
+    find_parser.add_argument('spec',
+                             nargs='+',
+                             help='spec to find a module file for.')
 
 
 def module_find(mtype, spec_array):
@@ -58,7 +56,8 @@ def module_find(mtype, spec_array):
        should type to use that package's module.
     """
     if mtype not in module_types:
-        tty.die("Invalid module type: '%s'.  Options are %s" % (mtype, comma_or(module_types)))
+        tty.die("Invalid module type: '%s'.  Options are %s" %
+                (mtype, comma_or(module_types)))
 
     specs = spack.cmd.parse_specs(spec_array)
     if len(specs) > 1:
@@ -94,11 +93,9 @@ def module_refresh():
             shutil.rmtree(cls.path, ignore_errors=False)
         mkdirp(cls.path)
         for spec in specs:
-            tty.debug("   Writing file for %s" % spec)
             cls(spec).write()
 
 
-
 def module(parser, args):
     if args.module_command == 'refresh':
         module_refresh()

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

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import re
 import cgi

lib/spack/spack/cmd/patch.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 

lib/spack/spack/cmd/pkg.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 

lib/spack/spack/cmd/providers.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import argparse

lib/spack/spack/cmd/purge.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import spack.stage as stage
 

lib/spack/spack/cmd/python.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import sys

lib/spack/spack/cmd/reindex.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import spack

lib/spack/spack/cmd/repo.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://software.llnl.gov/spack
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import re

lib/spack/spack/cmd/restage.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2014, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 

lib/spack/spack/cmd/spec.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import spack.cmd

lib/spack/spack/cmd/stage.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import argparse

lib/spack/spack/cmd/test-install.py

@@ -1,109 +1,128 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
-import xml.etree.ElementTree as ET
-import itertools
-import re
-import os
 import codecs
+import os
+import time
+import xml.dom.minidom
+import xml.etree.ElementTree as ET
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import *
-
 import spack
+import spack.cmd
+from llnl.util.filesystem import *
 from spack.build_environment import InstallError
 from spack.fetch_strategy import FetchError
-import spack.cmd
 
 description = "Run package installation as a unit test, output formatted results."
 
+
 def setup_parser(subparser):
-    subparser.add_argument(
+    subparser.add_argument('-j',
-        '-j', '--jobs', action='store', type=int,
+                           '--jobs',
+                           action='store',
+                           type=int,
                            help="Explicitly set number of make jobs.  Default is #cpus.")
 
-    subparser.add_argument(
+    subparser.add_argument('-n',
-        '-n', '--no-checksum', action='store_true', dest='no_checksum',
+                           '--no-checksum',
+                           action='store_true',
+                           dest='no_checksum',
                            help="Do not check packages against checksum")
 
-    subparser.add_argument(
+    subparser.add_argument('-o', '--output', action='store', help="test output goes in this file")
-        '-o', '--output', action='store', help="test output goes in this file")
 
-    subparser.add_argument(
+    subparser.add_argument('package', nargs=argparse.REMAINDER, help="spec of package to install")
-        'package', nargs=argparse.REMAINDER, help="spec of package to install")
-
-
-class JunitResultFormat(object):
-    def __init__(self):
-        self.root = ET.Element('testsuite')
-        self.tests = []
-
-    def add_test(self, buildId, testResult, buildInfo=None):
-        self.tests.append((buildId, testResult, buildInfo))
-
-    def write_to(self, stream):
-        self.root.set('tests', '{0}'.format(len(self.tests)))
-        for buildId, testResult, buildInfo in self.tests:
-            testcase = ET.SubElement(self.root, 'testcase')
-            testcase.set('classname', buildId.name)
-            testcase.set('name', buildId.stringId())
-            if testResult == TestResult.FAILED:
-                failure = ET.SubElement(testcase, 'failure')
-                failure.set('type', "Build Error")
-                failure.text = buildInfo
-            elif testResult == TestResult.SKIPPED:
-                skipped = ET.SubElement(testcase, 'skipped')
-                skipped.set('type', "Skipped Build")
-                skipped.text = buildInfo
-        ET.ElementTree(self.root).write(stream)
 
 
 class TestResult(object):
     PASSED = 0
     FAILED = 1
     SKIPPED = 2
+    ERRORED = 3
 
 
-class BuildId(object):
+class TestSuite(object):
-    def __init__(self, spec):
+    def __init__(self, filename):
-        self.name = spec.name
+        self.filename = filename
-        self.version = spec.version
+        self.root = ET.Element('testsuite')
-        self.hashId = spec.dag_hash()
+        self.tests = []
 
-    def stringId(self):
+    def __enter__(self):
-        return "-".join(str(x) for x in (self.name, self.version, self.hashId))
+        return self
 
-    def __hash__(self):
+    def append(self, item):
-        return hash((self.name, self.version, self.hashId))
+        if not isinstance(item, TestCase):
+            raise TypeError('only TestCase instances may be appended to a TestSuite instance')
+        self.tests.append(item)  # Append the item to the list of tests
 
-    def __eq__(self, other):
+    def __exit__(self, exc_type, exc_val, exc_tb):
-        if not isinstance(other, BuildId):
+        # Prepare the header for the entire test suite
-            return False
+        number_of_errors = sum(x.result_type == TestResult.ERRORED for x in self.tests)
+        self.root.set('errors', str(number_of_errors))
+        number_of_failures = sum(x.result_type == TestResult.FAILED for x in self.tests)
+        self.root.set('failures', str(number_of_failures))
+        self.root.set('tests', str(len(self.tests)))
 
-        return ((self.name, self.version, self.hashId) ==
+        for item in self.tests:
-            (other.name, other.version, other.hashId))
+            self.root.append(item.element)
+
+        with open(self.filename, 'wb') as file:
+            xml_string = ET.tostring(self.root)
+            xml_string = xml.dom.minidom.parseString(xml_string).toprettyxml()
+            file.write(xml_string)
+
+
+class TestCase(object):
+
+    results = {
+        TestResult.PASSED: None,
+        TestResult.SKIPPED: 'skipped',
+        TestResult.FAILED: 'failure',
+        TestResult.ERRORED: 'error',
+    }
+
+    def __init__(self, classname, name, time=None):
+        self.element = ET.Element('testcase')
+        self.element.set('classname', str(classname))
+        self.element.set('name', str(name))
+        if time is not None:
+            self.element.set('time', str(time))
+        self.result_type = None
+
+    def set_result(self, result_type, message=None, error_type=None, text=None):
+        self.result_type = result_type
+        result = TestCase.results[self.result_type]
+        if result is not None and result is not TestResult.PASSED:
+            subelement = ET.SubElement(self.element, result)
+            if error_type is not None:
+                subelement.set('type', error_type)
+            if message is not None:
+                subelement.set('message', str(message))
+            if text is not None:
+                subelement.text = text
 
 
 def fetch_log(path):
@@ -114,46 +133,76 @@ def fetch_log(path):
 
 
 def failed_dependencies(spec):
-    return set(childSpec for childSpec in spec.dependencies.itervalues() if not
+    return set(item for item in spec.dependencies.itervalues() if not spack.repo.get(item).installed)
-        spack.repo.get(childSpec).installed)
 
 
-def create_test_output(topSpec, newInstalls, output, getLogFunc=fetch_log):
+def get_top_spec_or_die(args):
-    # Post-order traversal is not strictly required but it makes sense to output
+    specs = spack.cmd.parse_specs(args.package, concretize=True)
-    # tests for dependencies first.
+    if len(specs) > 1:
-    for spec in topSpec.traverse(order='post'):
+        tty.die("Only 1 top-level package can be specified")
-        if spec not in newInstalls:
+    top_spec = iter(specs).next()
-            continue
+    return top_spec
 
-        failedDeps = failed_dependencies(spec)
+
+def install_single_spec(spec, number_of_jobs):
     package = spack.repo.get(spec)
-        if failedDeps:
-            result = TestResult.SKIPPED
-            dep = iter(failedDeps).next()
-            depBID = BuildId(dep)
-            errOutput = "Skipped due to failed dependency: {0}".format(
-                depBID.stringId())
-        elif (not package.installed) and (not package.stage.source_path):
-            result = TestResult.FAILED
-            errOutput = "Failure to fetch package resources."
-        elif not package.installed:
-            result = TestResult.FAILED
-            lines = getLogFunc(package.build_log_path)
-            errMessages = list(line for line in lines if
-                re.search('error:', line, re.IGNORECASE))
-            errOutput = errMessages if errMessages else lines[-10:]
-            errOutput = '\n'.join(itertools.chain(
-                    [spec.to_yaml(), "Errors:"], errOutput,
-                    ["Build Log:", package.build_log_path]))
-        else:
-            result = TestResult.PASSED
-            errOutput = None
 
-        bId = BuildId(spec)
+    # If it is already installed, skip the test
-        output.add_test(bId, result, errOutput)
+    if spack.repo.get(spec).installed:
+        testcase = TestCase(package.name, package.spec.short_spec, time=0.0)
+        testcase.set_result(TestResult.SKIPPED, message='Skipped [already installed]', error_type='already_installed')
+        return testcase
+
+    # If it relies on dependencies that did not install, skip
+    if failed_dependencies(spec):
+        testcase = TestCase(package.name, package.spec.short_spec, time=0.0)
+        testcase.set_result(TestResult.SKIPPED, message='Skipped [failed dependencies]', error_type='dep_failed')
+        return testcase
+
+    # Otherwise try to install the spec
+    try:
+        start_time = time.time()
+        package.do_install(keep_prefix=False,
+                           keep_stage=True,
+                           ignore_deps=False,
+                           make_jobs=number_of_jobs,
+                           verbose=True,
+                           fake=False)
+        duration = time.time() - start_time
+        testcase = TestCase(package.name, package.spec.short_spec, duration)
+        testcase.set_result(TestResult.PASSED)
+    except InstallError:
+        # An InstallError is considered a failure (the recipe didn't work correctly)
+        duration = time.time() - start_time
+        # Try to get the log
+        lines = fetch_log(package.build_log_path)
+        text = '\n'.join(lines)
+        testcase = TestCase(package.name, package.spec.short_spec, duration)
+        testcase.set_result(TestResult.FAILED, message='Installation failure', text=text)
+
+    except FetchError:
+        # A FetchError is considered an error (we didn't even start building)
+        duration = time.time() - start_time
+        testcase = TestCase(package.name, package.spec.short_spec, duration)
+        testcase.set_result(TestResult.ERRORED, message='Unable to fetch package')
+
+    return testcase
+
+
+def get_filename(args, top_spec):
+    if not args.output:
+        fname = 'test-{x.name}-{x.version}-{hash}.xml'.format(x=top_spec, hash=top_spec.dag_hash())
+        output_directory = join_path(os.getcwd(), 'test-output')
+        if not os.path.exists(output_directory):
+            os.mkdir(output_directory)
+        output_filename = join_path(output_directory, fname)
+    else:
+        output_filename = args.output
+    return output_filename
 
 
 def test_install(parser, args):
+    # Check the input
     if not args.package:
         tty.die("install requires a package argument")
 
@@ -164,48 +213,13 @@ def test_install(parser, args):
     if args.no_checksum:
         spack.do_checksum = False  # TODO: remove this global.
 
-    specs = spack.cmd.parse_specs(args.package, concretize=True)
+    # Get the one and only top spec
-    if len(specs) > 1:
+    top_spec = get_top_spec_or_die(args)
-        tty.die("Only 1 top-level package can be specified")
+    # Get the filename of the test
-    topSpec = iter(specs).next()
+    output_filename = get_filename(args, top_spec)
-
+    # TEST SUITE
-    newInstalls = set()
+    with TestSuite(output_filename) as test_suite:
-    for spec in topSpec.traverse():
+        # Traverse in post order : each spec is a test case
-        package = spack.repo.get(spec)
+        for spec in top_spec.traverse(order='post'):
-        if not package.installed:
+            test_case = install_single_spec(spec, args.jobs)
-            newInstalls.add(spec)
+            test_suite.append(test_case)
-
-    if not args.output:
-        bId = BuildId(topSpec)
-        outputDir = join_path(os.getcwd(), "test-output")
-        if not os.path.exists(outputDir):
-            os.mkdir(outputDir)
-        outputFpath = join_path(outputDir, "test-{0}.xml".format(bId.stringId()))
-    else:
-        outputFpath = args.output
-
-    for spec in topSpec.traverse(order='post'):
-        # Calling do_install for the top-level package would be sufficient but
-        # this attempts to keep going if any package fails (other packages which
-        # are not dependents may succeed)
-        package = spack.repo.get(spec)
-        if (not failed_dependencies(spec)) and (not package.installed):
-            try:
-                package.do_install(
-                    keep_prefix=False,
-                    keep_stage=True,
-                    ignore_deps=False,
-                    make_jobs=args.jobs,
-                    verbose=True,
-                    fake=False)
-            except InstallError:
-                pass
-            except FetchError:
-                pass
-
-    jrf = JunitResultFormat()
-    handled = {}
-    create_test_output(topSpec, newInstalls, jrf)
-
-    with open(outputFpath, 'wb') as F:
-            jrf.write_to(F)

lib/spack/spack/cmd/test.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 from pprint import pprint

lib/spack/spack/cmd/uninstall.py

@@ -1,41 +1,55 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from __future__ import print_function
-import sys
+
 import argparse
 
 import llnl.util.tty as tty
-from llnl.util.tty.colify import colify
-
 import spack
 import spack.cmd
 import spack.repository
 from spack.cmd.find import display_specs
-from spack.package import PackageStillNeededError
 
-description="Remove an installed package"
+description = "Remove an installed package"
+
+error_message = """You can either:
+    a) Use a more specific spec, or
+    b) use spack uninstall -a to uninstall ALL matching specs.
+"""
+
+
+def ask_for_confirmation(message):
+    while True:
+        tty.msg(message + '[y/n]')
+        choice = raw_input().lower()
+        if choice == 'y':
+            break
+        elif choice == 'n':
+            raise SystemExit('Operation aborted')
+        tty.warn('Please reply either "y" or "n"')
+
 
 def setup_parser(subparser):
     subparser.add_argument(
@@ -47,7 +61,98 @@ def setup_parser(subparser):
              "supplied spec. i.e., if you say uninstall libelf, ALL versions of " +
              "libelf are uninstalled. This is both useful and dangerous, like rm -r.")
     subparser.add_argument(
-        'packages', nargs=argparse.REMAINDER, help="specs of packages to uninstall")
+        '-d', '--dependents', action='store_true', dest='dependents',
+        help='Also uninstall any packages that depend on the ones given via command line.'
+    )
+    subparser.add_argument(
+        '-y', '--yes-to-all', action='store_true', dest='yes_to_all',
+        help='Assume "yes" is the answer to every confirmation asked to the user.'
+
+    )
+    subparser.add_argument('packages', nargs=argparse.REMAINDER, help="specs of packages to uninstall")
+
+
+def concretize_specs(specs, allow_multiple_matches=False, force=False):
+    """
+    Returns a list of specs matching the non necessarily concretized specs given from cli
+
+    Args:
+        specs: list of specs to be matched against installed packages
+        allow_multiple_matches : boolean (if True multiple matches for each item in specs are admitted)
+
+    Return:
+        list of specs
+    """
+    specs_from_cli = []  # List of specs that match expressions given via command line
+    has_errors = False
+    for spec in specs:
+        matching = spack.installed_db.query(spec)
+        # For each spec provided, make sure it refers to only one package.
+        # Fail and ask user to be unambiguous if it doesn't
+        if not allow_multiple_matches and len(matching) > 1:
+            tty.error("%s matches multiple packages:" % spec)
+            print()
+            display_specs(matching, long=True, show_flags=True)
+            print()
+            has_errors = True
+
+        # No installed package matches the query
+        if len(matching) == 0 and not force:
+            tty.error("%s does not match any installed packages." % spec)
+            has_errors = True
+
+        specs_from_cli.extend(matching)
+    if has_errors:
+        tty.die(error_message)
+
+    return specs_from_cli
+
+
+def installed_dependents(specs):
+    """
+    Returns a dictionary that maps a spec with a list of its installed dependents
+
+    Args:
+        specs: list of specs to be checked for dependents
+
+    Returns:
+        dictionary of installed dependents
+    """
+    dependents = {}
+    for item in specs:
+        lst = [x for x in item.package.installed_dependents if x not in specs]
+        if lst:
+            lst = list(set(lst))
+            dependents[item] = lst
+    return dependents
+
+
+def do_uninstall(specs, force):
+    """
+    Uninstalls all the specs in a list.
+
+    Args:
+        specs: list of specs to be uninstalled
+        force: force uninstallation (boolean)
+    """
+    packages = []
+    for item in specs:
+        try:
+            # should work if package is known to spack
+            packages.append(item.package)
+        except spack.repository.UnknownPackageError as e:
+            # The package.py file has gone away -- but still
+            # want to uninstall.
+            spack.Package(item).do_uninstall(force=True)
+
+    # Sort packages to be uninstalled by the number of installed dependents
+    # This ensures we do things in the right order
+    def num_installed_deps(pkg):
+        return len(pkg.installed_dependents)
+
+    packages.sort(key=num_installed_deps)
+    for item in packages:
+        item.do_uninstall(force=force)
 
 
 def uninstall(parser, args):
@@ -56,50 +161,34 @@ def uninstall(parser, args):
 
     with spack.installed_db.write_transaction():
         specs = spack.cmd.parse_specs(args.packages)
+        # Gets the list of installed specs that match the ones give via cli
+        uninstall_list = concretize_specs(specs, args.all, args.force)  # takes care of '-a' is given in the cli
+        dependent_list = installed_dependents(uninstall_list)  # takes care of '-d'
 
-        # For each spec provided, make sure it refers to only one package.
+        # Process dependent_list and update uninstall_list
-        # Fail and ask user to be unambiguous if it doesn't
+        has_error = False
-        pkgs = []
+        if dependent_list and not args.dependents and not args.force:
-        for spec in specs:
+            for spec, lst in dependent_list.items():
-            matching_specs = spack.installed_db.query(spec)
+                tty.error("Will not uninstall %s" % spec.format("$_$@$%@$#", color=True))
-            if not args.all and len(matching_specs) > 1:
-                tty.error("%s matches multiple packages:" % spec)
-                print()
-                display_specs(matching_specs, long=True)
-                print()
-                print("You can either:")
-                print("  a) Use a more specific spec, or")
-                print("  b) use spack uninstall -a to uninstall ALL matching specs.")
-                sys.exit(1)
-
-            if len(matching_specs) == 0:
-                if args.force: continue
-                tty.die("%s does not match any installed packages." % spec)
-
-            for s in matching_specs:
-                try:
-                    # should work if package is known to spack
-                    pkgs.append(s.package)
-                except spack.repository.UnknownPackageError as e:
-                    # The package.py file has gone away -- but still
-                    # want to uninstall.
-                    spack.Package(s).do_uninstall(force=True)
-
-        # Sort packages to be uninstalled by the number of installed dependents
-        # This ensures we do things in the right order
-        def num_installed_deps(pkg):
-            return len(pkg.installed_dependents)
-        pkgs.sort(key=num_installed_deps)
-
-        # Uninstall packages in order now.
-        for pkg in pkgs:
-            try:
-                pkg.do_uninstall(force=args.force)
-            except PackageStillNeededError as e:
-                tty.error("Will not uninstall %s" % e.spec.format("$_$@$%@$#", color=True))
                 print('')
                 print("The following packages depend on it:")
-                display_specs(e.dependents, long=True)
+                display_specs(lst, long=True)
                 print('')
-                print("You can use spack uninstall -f to force this action.")
+                has_error = True
-                sys.exit(1)
+        elif args.dependents:
+            for key, lst in dependent_list.items():
+                uninstall_list.extend(lst)
+            uninstall_list = list(set(uninstall_list))
+
+        if has_error:
+            tty.die('You can use spack uninstall --dependents to uninstall these dependencies as well')
+
+        if not args.yes_to_all:
+            tty.msg("The following packages will be uninstalled : ")
+            print('')
+            display_specs(uninstall_list, long=True, show_flags=True)
+            print('')
+            ask_for_confirmation('Do you want to proceed ? ')
+
+        # Uninstall everything on the list
+        do_uninstall(uninstall_list, args.force)

lib/spack/spack/cmd/unload.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by David Beckingsale, david@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import spack.modules

lib/spack/spack/cmd/unuse.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import spack.modules

lib/spack/spack/cmd/url-parse.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
 

lib/spack/spack/cmd/urls.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
 import spack

lib/spack/spack/cmd/use.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import argparse
 import spack.modules

lib/spack/spack/cmd/versions.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 from llnl.util.tty.colify import colify

lib/spack/spack/compiler.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import re
@@ -91,14 +91,25 @@ class Compiler(object):
     # version suffix for gcc.
     suffixes = [r'-.*']
 
-    # Names of generic arguments used by this compiler
+    # Default flags used by a compiler to set an rpath
-    arg_rpath   = '-Wl,-rpath,%s'
+    @property
+    def cc_rpath_arg(self):
+        return '-Wl,-rpath,'
 
-    # argument used to get C++11 options
+    @property
-    cxx11_flag = "-std=c++11"
+    def cxx_rpath_arg(self):
+        return '-Wl,-rpath,'
+
+    @property
+    def f77_rpath_arg(self):
+        return '-Wl,-rpath,'
+
+    @property
+    def fc_rpath_arg(self):
+        return '-Wl,-rpath,'
 
 
-    def __init__(self, cspec, cc, cxx, f77, fc):
+    def __init__(self, cspec, cc, cxx, f77, fc, **kwargs):
         def check(exe):
             if exe is None:
                 return None
@@ -110,6 +121,15 @@ def check(exe):
         self.f77 = check(f77)
         self.fc  = check(fc)
 
+        # Unfortunately have to make sure these params are accepted
+        # in the same order they are returned by sorted(flags)
+        # in compilers/__init__.py
+        self.flags = {}
+        for flag in spack.spec.FlagMap.valid_compiler_flags():
+            value = kwargs.get(flag, None)
+            if value is not None:
+                self.flags[flag] = value.split()
+
         self.spec = cspec
 
 
@@ -117,6 +137,37 @@ def check(exe):
     def version(self):
         return self.spec.version
 
+    # This property should be overridden in the compiler subclass if
+    # OpenMP is supported by that compiler
+    @property
+    def openmp_flag(self):
+        # If it is not overridden, assume it is not supported and warn the user
+        tty.die("The compiler you have chosen does not currently support OpenMP.",
+                "If you think it should, please edit the compiler subclass and",
+                "submit a pull request or issue.")
+
+
+    # This property should be overridden in the compiler subclass if
+    # C++11 is supported by that compiler
+    @property
+    def cxx11_flag(self):
+        # If it is not overridden, assume it is not supported and warn the user
+        tty.die("The compiler you have chosen does not currently support C++11.",
+                "If you think it should, please edit the compiler subclass and",
+                "submit a pull request or issue.")
+
+
+    # This property should be overridden in the compiler subclass if
+    # C++14 is supported by that compiler
+    @property
+    def cxx14_flag(self):
+        # If it is not overridden, assume it is not supported and warn the user
+        tty.die("The compiler you have chosen does not currently support C++14.",
+                "If you think it should, please edit the compiler subclass and",
+                "submit a pull request or issue.")
+
+
+
     #
     # Compiler classes have methods for querying the version of
     # specific compiler executables.  This is used when discovering compilers.
@@ -146,7 +197,6 @@ def f77_version(cls, f77):
     def fc_version(cls, fc):
         return cls.default_version(fc)
 
-
     @classmethod
     def _find_matches_in_path(cls, compiler_names, detect_version, *path):
         """Finds compilers in the paths supplied.
@@ -202,6 +252,10 @@ def check(key):
                 return None
 
         successful = [key for key in parmap(check, checks) if key is not None]
+        # The 'successful' list is ordered like the input paths.
+        # Reverse it here so that the dict creation (last insert wins)
+        # does not spoil the intented precedence.
+        successful.reverse()
         return dict(((v, p, s), path) for v, p, s, path in successful)
 
     @classmethod

lib/spack/spack/compilers/__init__.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """This module contains functions related to finding compilers on the
 system and configuring Spack to use multiple compilers.
@@ -255,7 +255,11 @@ def get_compiler(cspec):
             else:
                 compiler_paths.append(None)
 
-        return cls(cspec, *compiler_paths)
+        flags = {}
+        for f in spack.spec.FlagMap.valid_compiler_flags():
+            if f in items:
+                flags[f] = items[f]
+        return cls(cspec, *compiler_paths, **flags)
 
     matches = find(compiler_spec, arch, scope)
     return [get_compiler(cspec) for cspec in matches]

lib/spack/spack/compilers/clang.py

@@ -1,31 +1,33 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import re
 import spack.compiler as cpr
 from spack.compiler import *
 from spack.util.executable import *
+import llnl.util.tty as tty
+from spack.version import ver
 
 class Clang(Compiler):
     # Subclasses use possible names of C compiler
@@ -47,6 +49,29 @@ class Clang(Compiler):
                    'f77' : 'f77',
                    'fc'  : 'f90' }
 
+    @property
+    def is_apple(self):
+        ver_string = str(self.version)
+        return ver_string.endswith('-apple')
+
+    @property
+    def openmp_flag(self):
+        if self.is_apple:
+            tty.die("Clang from Apple does not support Openmp yet.")
+        else:
+            return "-fopenmp"
+
+    @property
+    def cxx11_flag(self):
+        if self.is_apple:
+            # FIXME: figure out from which version Apple's clang supports c++11
+            return "-std=c++11"
+        else:
+            if self.version < ver('3.3'):
+                tty.die("Only Clang 3.3 and above support c++11.")
+            else:
+                return "-std=c++11"
+
     @classmethod
     def default_version(self, comp):
         """The '--version' option works for clang compilers.

lib/spack/spack/compilers/gcc.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import llnl.util.tty as tty
 from spack.compiler import *
@@ -49,14 +49,25 @@ class Gcc(Compiler):
                   'f77' : 'gcc/gfortran',
                   'fc'  : 'gcc/gfortran' }
 
+    @property
+    def openmp_flag(self):
+        return "-fopenmp"
+
     @property
     def cxx11_flag(self):
         if self.version < ver('4.3'):
             tty.die("Only gcc 4.3 and above support c++11.")
         elif self.version < ver('4.7'):
-            return "-std=gnu++0x"
+            return "-std=c++0x"
         else:
-            return "-std=gnu++11"
+            return "-std=c++11"
+
+    @property
+    def cxx14_flag(self):
+        if self.version < ver('4.8'):
+            tty.die("Only gcc 4.8 and above support c++14.")
+        else:
+            return "-std=c++14"
 
     @classmethod
     def fc_version(cls, fc):

lib/spack/spack/compilers/intel.py

@@ -1,28 +1,30 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack.compiler import *
+import llnl.util.tty as tty
+from spack.version import ver
 
 class Intel(Compiler):
     # Subclasses use possible names of C compiler
@@ -43,6 +45,13 @@ class Intel(Compiler):
                    'f77' : 'intel/ifort',
                    'fc'  : 'intel/ifort' }
 
+    @property
+    def openmp_flag(self):
+        if self.version < ver('16.0'):
+            return "-openmp"
+        else:
+            return "-qopenmp"
+
     @property
     def cxx11_flag(self):
         if self.version < ver('11.1'):
@@ -68,5 +77,3 @@ def default_version(cls, comp):
         """
         return get_compiler_version(
             comp, '--version', r'\((?:IFORT|ICC)\) ([^ ]+)')
-
-

lib/spack/spack/compilers/nag.py

@@ -1,4 +1,29 @@
+##############################################################################
+# 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.compiler import *
+import llnl.util.tty as tty
 
 class Nag(Compiler):
     # Subclasses use possible names of C compiler
@@ -20,6 +45,27 @@ class Nag(Compiler):
                    'f77' : 'nag/nagfor',
                    'fc'  : 'nag/nagfor' }
 
+    @property
+    def openmp_flag(self):
+        return "-openmp"
+
+    @property
+    def cxx11_flag(self):
+        # NAG does not have a C++ compiler
+        # However, it can be mixed with a compiler that does support it
+        return "-std=c++11"
+
+    # Unlike other compilers, the NAG compiler passes options to GCC, which
+    # then passes them to the linker. Therefore, we need to doubly wrap the
+    # options with '-Wl,-Wl,,'
+    @property
+    def f77_rpath_arg(self):
+        return '-Wl,-Wl,,-rpath,'
+
+    @property
+    def fc_rpath_arg(self):
+        return '-Wl,-Wl,,-rpath,'
+
     @classmethod
     def default_version(self, comp):
         """The '-V' option works for nag compilers.

lib/spack/spack/compilers/pgi.py

@@ -1,28 +1,29 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack.compiler import *
+import llnl.util.tty as tty
 
 class Pgi(Compiler):
     # Subclasses use possible names of C compiler
@@ -43,6 +44,15 @@ class Pgi(Compiler):
                    'f77' : 'pgi/pgfortran',
                    'fc'  : 'pgi/pgfortran' }
 
+    @property
+    def openmp_flag(self):
+        return "-mp"
+
+    @property
+    def cxx11_flag(self):
+        return "-std=c++11"
+
+
     @classmethod
     def default_version(cls, comp):
         """The '-V' option works for all the PGI compilers.
@@ -54,4 +64,3 @@ def default_version(cls, comp):
         """
         return get_compiler_version(
             comp, '-V', r'pg[^ ]* ([^ ]+) \d\d\d?-bit target')
-

lib/spack/spack/compilers/xl.py

@@ -1,29 +1,30 @@
-# -*- coding: utf-8 -*-
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by François Bissey, francois.bissey@canterbury.ac.nz, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack.compiler import *
+import llnl.util.tty as tty
+from spack.version import ver
 
 class Xl(Compiler):
     # Subclasses use possible names of C compiler
@@ -44,6 +45,10 @@ class Xl(Compiler):
                    'f77' : 'xl/xlf',
                    'fc'  : 'xl/xlf90' }
 
+    @property
+    def openmp_flag(self):
+        return "-qsmp=omp"
+
     @property
     def cxx11_flag(self):
         if self.version < ver('13.1'):

lib/spack/spack/concretize.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 Functions here are used to take abstract specs and make them concrete.
@@ -44,6 +44,7 @@
 from itertools import chain
 from spack.config import *
 
+
 class DefaultConcretizer(object):
     """This class doesn't have any state, it just provides some methods for
        concretization.  You can subclass it to override just some of the
@@ -269,6 +270,59 @@ def concretize_compiler(self, spec):
         return True  # things changed.
 
 
+    def concretize_compiler_flags(self, spec):
+        """
+        The compiler flags are updated to match those of the spec whose
+        compiler is used, defaulting to no compiler flags in the spec.
+        Default specs set at the compiler level will still be added later.
+        """
+        ret = False
+        for flag in spack.spec.FlagMap.valid_compiler_flags():
+            try:
+                nearest = next(p for p in spec.traverse(direction='parents')
+                               if ((p.compiler == spec.compiler and p is not spec)
+                               and flag in p.compiler_flags))
+                if ((not flag in spec.compiler_flags) or
+                    sorted(spec.compiler_flags[flag]) != sorted(nearest.compiler_flags[flag])):
+                    if flag in spec.compiler_flags:
+                        spec.compiler_flags[flag] = list(set(spec.compiler_flags[flag]) |
+                                                         set(nearest.compiler_flags[flag]))
+                    else:
+                        spec.compiler_flags[flag] = nearest.compiler_flags[flag]
+                    ret = True
+
+            except StopIteration:
+                if (flag in spec.root.compiler_flags and ((not flag in spec.compiler_flags) or
+                    sorted(spec.compiler_flags[flag]) != sorted(spec.root.compiler_flags[flag]))):
+                    if flag in spec.compiler_flags:
+                        spec.compiler_flags[flag] = list(set(spec.compiler_flags[flag]) |
+                                                         set(spec.root.compiler_flags[flag]))
+                    else:
+                        spec.compiler_flags[flag] = spec.root.compiler_flags[flag]
+                    ret = True
+                else:
+                    if not flag in spec.compiler_flags:
+                        spec.compiler_flags[flag] = []
+
+        # Include the compiler flag defaults from the config files
+        # This ensures that spack will detect conflicts that stem from a change
+        # in default compiler flags.
+        compiler = spack.compilers.compiler_for_spec(spec.compiler)
+        for flag in compiler.flags:
+            if flag not in spec.compiler_flags:
+                spec.compiler_flags[flag] = compiler.flags[flag]
+                if compiler.flags[flag] != []:
+                    ret = True
+            else:
+                if ((sorted(spec.compiler_flags[flag]) != sorted(compiler.flags[flag])) and
+                    (not set(spec.compiler_flags[flag]) >= set(compiler.flags[flag]))):
+                    ret = True
+                    spec.compiler_flags[flag] = list(set(spec.compiler_flags[flag]) |
+                                                     set(compiler.flags[flag]))
+
+        return ret
+
+
 def find_spec(spec, condition):
     """Searches the dag from spec in an intelligent order and looks
        for a spec that matches a condition"""
@@ -330,7 +384,6 @@ def cmp_specs(lhs, rhs):
     return 0
 
 
-
 class UnavailableCompilerVersionError(spack.error.SpackError):
     """Raised when there is no available compiler that satisfies a
        compiler spec."""

lib/spack/spack/config.py

@@ -1,26 +1,27 @@
+# flake8: noqa
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """This module implements Spack's configuration file handling.
 
@@ -117,22 +118,20 @@
 the site configuration will be ignored.
 
 """
+import copy
 import os
 import re
 import sys
-import copy
+
 import jsonschema
-from jsonschema import Draft4Validator, validators
-import yaml
-from yaml.error import MarkedYAMLError
-from ordereddict_backport import OrderedDict
-
 import llnl.util.tty as tty
-from llnl.util.filesystem import mkdirp
-import copy
-
 import spack
+import yaml
+from jsonschema import Draft4Validator, validators
+from llnl.util.filesystem import mkdirp
+from ordereddict_backport import OrderedDict
 from spack.error import SpackError
+from yaml.error import MarkedYAMLError
 
 # Hacked yaml for configuration files preserves line numbers.
 import spack.util.spack_yaml as syaml
@@ -195,6 +194,7 @@
                 'default': [],
                 'items': {
                     'type': 'string'},},},},
+
     'packages': {
         '$schema': 'http://json-schema.org/schema#',
         'title': 'Spack package configuration file schema',
@@ -238,18 +238,43 @@
                                 'default' : {},
                             }
                         },},},},},},
+
     'modules': {
         '$schema': 'http://json-schema.org/schema#',
         'title': 'Spack module file configuration file schema',
         'type': 'object',
         'additionalProperties': False,
+        'definitions': {
+            'array_of_strings': {
+                'type': 'array',
+                'default': [],
+                'items': {
+                    'type': 'string'
+                }
+            },
+            'dictionary_of_strings': {
+                'type': 'object',
                 'patternProperties': {
-            r'modules:?': {
+                    r'\w[\w-]*': {  # key
+                        'type': 'string'
+                    }
+                }
+            },
+            'dependency_selection': {
+                'type': 'string',
+                'enum': ['none', 'direct', 'all']
+            },
+            'module_file_configuration': {
                 'type': 'object',
                 'default': {},
                 'additionalProperties': False,
                 'properties': {
-                    'enable': {
+                    'filter': {
+                        'type': 'object',
+                        'default': {},
+                        'additionalProperties': False,
+                        'properties': {
+                            'environment_blacklist': {
                                 'type': 'array',
                                 'default': [],
                                 'items': {
@@ -258,6 +283,77 @@
                             }
                         }
                     },
+                    'autoload': {'$ref': '#/definitions/dependency_selection'},
+                    'prerequisites': {'$ref': '#/definitions/dependency_selection'},
+                    'conflict': {'$ref': '#/definitions/array_of_strings'},
+                    'environment': {
+                        'type': 'object',
+                        'default': {},
+                        'additionalProperties': False,
+                        'properties': {
+                            'set': {'$ref': '#/definitions/dictionary_of_strings'},
+                            'unset': {'$ref': '#/definitions/array_of_strings'},
+                            'prepend_path': {'$ref': '#/definitions/dictionary_of_strings'},
+                            'append_path': {'$ref': '#/definitions/dictionary_of_strings'}
+                        }
+                    }
+                }
+            },
+            'module_type_configuration': {
+                'type': 'object',
+                'default': {},
+                'anyOf': [
+                    {
+                        'properties': {
+                            'whitelist': {'$ref': '#/definitions/array_of_strings'},
+                            'blacklist': {'$ref': '#/definitions/array_of_strings'},
+                            'naming_scheme': {
+                                'type': 'string'  # Can we be more specific here?
+                            }
+                        }
+                    },
+                    {
+                        'patternProperties': {r'\w[\w-]*': {'$ref': '#/definitions/module_file_configuration'}}
+                    }
+                ]
+            }
+        },
+        'patternProperties': {
+            r'modules:?': {
+                'type': 'object',
+                'default': {},
+                'additionalProperties': False,
+                'properties': {
+                    'prefix_inspections': {
+                        'type': 'object',
+                        'patternProperties': {
+                            r'\w[\w-]*': {  # path to be inspected for existence (relative to prefix)
+                                '$ref': '#/definitions/array_of_strings'
+                            }
+                        }
+                    },
+                    'enable': {
+                        'type': 'array',
+                        'default': [],
+                        'items': {
+                            'type': 'string',
+                            'enum': ['tcl', 'dotkit']
+                        }
+                    },
+                    'tcl': {
+                        'allOf': [
+                            {'$ref': '#/definitions/module_type_configuration'},  # Base configuration
+                            {}  # Specific tcl extensions
+                        ]
+                    },
+                    'dotkit': {
+                        'allOf': [
+                            {'$ref': '#/definitions/module_type_configuration'},  # Base configuration
+                            {}  # Specific dotkit extensions
+                        ]
+                    },
+                }
+            },
         },
     },
 }
@@ -269,10 +365,10 @@
 
 
 def validate_section_name(section):
-    """Raise a ValueError if the section is not a valid section."""
+    """Exit if the section is not a valid section."""
     if section not in section_schemas:
-        raise ValueError("Invalid config section: '%s'.  Options are %s"
+        tty.die("Invalid config section: '%s'. Options are: %s"
-                         % (section, section_schemas))
+                % (section, " ".join(section_schemas.keys())))
 
 
 def extend_with_default(validator_class):
@@ -306,13 +402,14 @@ def set_pp_defaults(validator, properties, instance, schema):
             yield err
 
     return validators.extend(validator_class, {
-        "properties" : set_defaults,
+        "properties": set_defaults,
-        "patternProperties" : set_pp_defaults
+        "patternProperties": set_pp_defaults
     })
 
 
 DefaultSettingValidator = extend_with_default(Draft4Validator)
 
+
 def validate_section(data, schema):
     """Validate data read in from a Spack YAML file.
 
@@ -347,16 +444,14 @@ def get_section_filename(self, section):
         validate_section_name(section)
         return os.path.join(self.path, "%s.yaml" % section)
 
-
     def get_section(self, section):
-        if not section in self.sections:
+        if section not in self.sections:
             path   = self.get_section_filename(section)
             schema = section_schemas[section]
             data   = _read_config_file(path, schema)
             self.sections[section] = data
         return self.sections[section]
 
-
     def write_section(self, section):
         filename = self.get_section_filename(section)
         data = self.get_section(section)
@@ -370,7 +465,6 @@ def write_section(self, section):
         except (yaml.YAMLError, IOError) as e:
             raise ConfigFileError("Error writing to config file: '%s'" % str(e))
 
-
     def clear(self):
         """Empty cached config information."""
         self.sections = {}
@@ -413,7 +507,7 @@ def _read_config_file(filename, schema):
 
     elif not os.path.isfile(filename):
         raise ConfigFileError(
-            "Invlaid configuration. %s exists but is not a file." % filename)
+            "Invalid configuration. %s exists but is not a file." % filename)
 
     elif not os.access(filename, os.R_OK):
         raise ConfigFileError("Config file is not readable: %s" % filename)
@@ -476,7 +570,7 @@ def they_are(t):
     # Source dict is merged into dest.
     elif they_are(dict):
         for sk, sv in source.iteritems():
-            if not sk in dest:
+            if sk not in dest:
                 dest[sk] = copy.copy(sv)
             else:
                 dest[sk] = _merge_yaml(dest[sk], source[sk])
@@ -539,14 +633,19 @@ def update_config(section, update_data, scope=None):
        other yaml-ish structure.
 
     """
-    # read in the config to ensure we've got current data
-    get_config(section)
-
     validate_section_name(section)  # validate section name
     scope = validate_scope(scope)  # get ConfigScope object from string.
 
+    # read in the config to ensure we've got current data
+    configuration = get_config(section)
+
+    if isinstance(update_data, list):
+        configuration = update_data
+    else:
+        configuration.update(update_data)
+
     # read only the requested section's data.
-    scope.sections[section] = { section : update_data }
+    scope.sections[section] = {section: configuration}
     scope.write_section(section)
 
 
@@ -585,16 +684,20 @@ def spec_externals(spec):
 def is_spec_buildable(spec):
     """Return true if the spec pkgspec is configured as buildable"""
     allpkgs = get_config('packages')
-    name = spec.name
+    if spec.name not in allpkgs:
-    if not spec.name in allpkgs:
         return True
-    if not 'buildable' in allpkgs[spec.name]:
+    if 'buildable' not in allpkgs[spec.name]:
         return True
     return allpkgs[spec.name]['buildable']
 
 
-class ConfigError(SpackError): pass
+class ConfigError(SpackError):
-class ConfigFileError(ConfigError): pass
+    pass
+
+
+class ConfigFileError(ConfigError):
+    pass
+
 
 def get_path(path, data):
     if path:
@@ -602,6 +705,7 @@ def get_path(path, data):
     else:
         return data
 
+
 class ConfigFormatError(ConfigError):
     """Raised when a configuration format does not match its schema."""
     def __init__(self, validation_error, data):
@@ -636,5 +740,6 @@ def __init__(self, validation_error, data):
         message = '%s: %s' % (location, validation_error.message)
         super(ConfigError, self).__init__(message)
 
+
 class ConfigSanityError(ConfigFormatError):
     """Same as ConfigFormatError, raised when config is written by Spack."""

lib/spack/spack/database.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """Spack's installation tracking database.
 
@@ -40,7 +40,6 @@
 
 """
 import os
-import time
 import socket
 
 import yaml
@@ -56,11 +55,12 @@
 from spack.error import SpackError
 from spack.repository import UnknownPackageError
 
+
 # DB goes in this directory underneath the root
 _db_dirname = '.spack-db'
 
 # DB version.  This is stuck in the DB file to track changes in format.
-_db_version = Version('0.9')
+_db_version = Version('0.9.1')
 
 # Default timeout for spack database locks is 5 min.
 _db_lock_timeout = 60
@@ -69,10 +69,12 @@
 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
 
 
@@ -92,22 +94,28 @@ class InstallRecord(object):
     dependents left.
 
     """
-    def __init__(self, spec, path, installed, ref_count=0):
+
+    def __init__(self, spec, path, installed, ref_count=0, explicit=False):
         self.spec = spec
         self.path = str(path)
         self.installed = bool(installed)
         self.ref_count = ref_count
+        self.explicit = explicit
 
     def to_dict(self):
-        return { 'spec'      : self.spec.to_node_dict(),
+        return {
-                 'path'      : self.path,
+            'spec': self.spec.to_node_dict(),
-                 'installed' : self.installed,
+            'path': self.path,
-                 'ref_count' : self.ref_count }
+            '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'])
+        return InstallRecord(spec, d['path'], d['installed'], d['ref_count'],
+                             d.get('explicit', False))
 
 
 class Database(object):
@@ -155,17 +163,14 @@ def __init__(self, root, db_dir=None):
         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.
 
@@ -181,9 +186,9 @@ def _write_to_yaml(self, stream):
         # different paths, it can't differentiate.
         # TODO: fix this before we support multiple install locations.
         database = {
-            'database' : {
+            'database': {
-                'installs' : installs,
+                'installs': installs,
-                'version' : str(_db_version)
+                'version': str(_db_version)
             }
         }
 
@@ -192,17 +197,18 @@ def _write_to_yaml(self, stream):
         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
+        # to ensure it is read properly.
+        for name in spec_dict:
+            spec_dict[name]['hash'] = hash_key
+
         # Build spec from dict first.
         spec = Spec.from_node_dict(spec_dict)
 
@@ -217,7 +223,6 @@ def _read_spec_from_yaml(self, hash_key, installs, parent_key=None):
         spec._mark_concrete()
         return spec
 
-
     def _read_from_yaml(self, stream):
         """
         Fill database from YAML, do not maintain old data
@@ -239,7 +244,8 @@ def _read_from_yaml(self, stream):
             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.")
 
@@ -248,13 +254,17 @@ def check(cond, msg):
         check('installs' in db, "No 'installs' in YAML DB.")
         check('version' in db, "No 'version' in YAML DB.")
 
+        installs = db['installs']
+
         # TODO: better version checking semantics.
         version = Version(db['version'])
-        if version != _db_version:
+        if version > _db_version:
             raise InvalidDatabaseVersionError(_db_version, version)
+        elif version < _db_version:
+            self.reindex(spack.install_layout)
+            installs = dict((k, v.to_dict()) for k, v in self._data.items())
 
         # Iterate through database and check each record.
-        installs = db['installs']
         data = {}
         for hash_key, rec in installs.items():
             try:
@@ -265,25 +275,25 @@ def check(cond, msg):
                 # 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"
+                    tty.warn(
-                             % (hash_key, spec_hash))
+                        "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,
+                         "hash:  %s" % hash_key, "cause: %s" % str(e))
-                         "cause: %s" % str(e))
                 raise
 
         self._data = data
 
-
     def reindex(self, directory_layout):
         """Build database index from scratch based from a directory layout.
 
@@ -308,7 +318,6 @@ def reindex(self, directory_layout):
                 self._data = old_data
                 raise
 
-
     def _check_ref_counts(self):
         """Ensure consistency of reference counts in the DB.
 
@@ -330,9 +339,8 @@ def _check_ref_counts(self):
             found = rec.ref_count
             if not expected == found:
                 raise AssertionError(
-                    "Invalid ref_count: %s: %d (expected %d), in DB %s"
+                    "Invalid ref_count: %s: %d (expected %d), in DB %s" %
-                    % (key, found, expected, self._index_path))
+                    (key, found, expected, self._index_path))
-
 
     def _write(self):
         """Write the in-memory database index to its file path.
@@ -354,7 +362,6 @@ def _write(self):
                 os.remove(temp_file)
             raise
 
-
     def _read(self):
         """Re-read Database from the data in the set location.
 
@@ -369,8 +376,7 @@ def _read(self):
             # 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):
-    def _add(self, spec, path, directory_layout=None):
         """Add an install record for spec at path to the database.
 
         This assumes that the spec is not already installed. It
@@ -392,11 +398,11 @@ def _add(self, spec, path, directory_layout=None):
             rec.path = path
 
         else:
-            self._data[key] = InstallRecord(spec, path, True)
+            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()
@@ -415,7 +421,7 @@ def _increment_ref_count(self, spec, directory_layout=None):
         self._data[key].ref_count += 1
 
     @_autospec
-    def add(self, spec, path):
+    def add(self, spec, path, explicit=False):
         """Add spec at path to database, locking and reading DB to sync.
 
         ``add()`` will lock and read from the DB on disk.
@@ -424,30 +430,27 @@ def add(self, spec, path):
         # TODO: ensure that spec is concrete?
         # Entire add is transactional.
         with self.write_transaction():
-            self._add(spec, path)
+            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
@@ -460,7 +463,6 @@ def _decrement_ref_count(self, spec):
             for dep in spec.dependencies.values():
                 self._decrement_ref_count(dep)
 
-
     def _remove(self, spec):
         """Non-locking version of remove(); does real work.
         """
@@ -479,7 +481,6 @@ def _remove(self, spec):
         # query spec was passed in.
         return rec.spec
 
-
     @_autospec
     def remove(self, spec):
         """Removes a spec from the database.  To be called on uninstall.
@@ -496,7 +497,6 @@ def remove(self, spec):
         with self.write_transaction():
             return self._remove(spec)
 
-
     @_autospec
     def installed_extensions_for(self, extendee_spec):
         """
@@ -507,13 +507,12 @@ def installed_extensions_for(self, extendee_spec):
             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):
-    def query(self, query_spec=any, known=any, installed=True):
         """Run a query on the database.
 
         ``query_spec``
@@ -553,14 +552,16 @@ def query(self, query_spec=any, known=any, installed=True):
             for key, rec in self._data.items():
                 if installed is not any and rec.installed != installed:
                     continue
-                if known is not any and spack.repo.exists(rec.spec.name) != known:
+                if explicit is not any and rec.explicit != explicit:
+                    continue
+                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.
 
@@ -572,7 +573,6 @@ def query_one(self, query_spec, known=any, installed=True):
         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()
@@ -587,7 +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
@@ -622,11 +625,11 @@ def _exit(self):
 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 database version %s but found version %s" %
-            % (expected, found))
+            (expected, found))

lib/spack/spack/directives.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """This package contains directives that can be used within a package.
 
@@ -45,11 +45,8 @@ class OpenMpi(Package):
   * ``resource``
 
 """
-__all__ = ['depends_on', 'extends', 'provides', 'patch', 'version',
-           'variant', 'resource']
 
 import re
-import inspect
 import os.path
 import functools
 
@@ -67,6 +64,9 @@ class OpenMpi(Package):
 from spack.resource import Resource
 from spack.fetch_strategy import from_kwargs
 
+__all__ = ['depends_on', 'extends', 'provides', 'patch', 'version', 'variant',
+           'resource']
+
 #
 # This is a list of all directives, built up as they are defined in
 # this file.
@@ -122,15 +122,14 @@ class Foo(Package):
 
     def __init__(self, dicts=None):
         if isinstance(dicts, basestring):
-            dicts = (dicts,)
+            dicts = (dicts, )
         elif type(dicts) not in (list, tuple):
             raise TypeError(
-                "dicts arg must be list, tuple, or string. Found %s"
+                "dicts arg must be list, tuple, or string. Found %s" %
-                % type(dicts))
+                type(dicts))
 
         self.dicts = dicts
 
-
     def ensure_dicts(self, pkg):
         """Ensure that a package has the dicts required by this directive."""
         for d in self.dicts:
@@ -142,7 +141,6 @@ def ensure_dicts(self, pkg):
                 raise spack.error.SpackError(
                     "Package %s has non-dict %s attribute!" % (pkg, d))
 
-
     def __call__(self, directive_function):
         directives[directive_function.__name__] = self
 
@@ -263,7 +261,8 @@ def variant(pkg, name, default=False, description=""):
     description = str(description).strip()
 
     if not re.match(spack.spec.identifier_re, name):
-        raise DirectiveError("Invalid variant name in %s: '%s'" % (pkg.name, name))
+        raise DirectiveError("Invalid variant name in %s: '%s'" %
+                             (pkg.name, name))
 
     pkg.variants[name] = Variant(default, description)
 
@@ -271,31 +270,37 @@ def variant(pkg, name, default=False, description=""):
 @directive('resources')
 def resource(pkg, **kwargs):
     """
-    Define an external resource to be fetched and staged when building the package. Based on the keywords present in the
+    Define an external resource to be fetched and staged when building the
-    dictionary the appropriate FetchStrategy will be used for the resource. Resources are fetched and staged in their
+    package. Based on the keywords present in the dictionary the appropriate
-    own folder inside spack stage area, and then linked into the stage area of the package that needs them.
+    FetchStrategy will be used for the resource. Resources are fetched and
+    staged in their own folder inside spack stage area, and then linked into
+    the stage area of the package that needs them.
 
     List of recognized keywords:
 
-    * 'when' : (optional) represents the condition upon which the resource is needed
+    * 'when' : (optional) represents the condition upon which the resource is
-    * 'destination' : (optional) path where to link the resource. This path must be relative to the main package stage
+    needed
-    area.
+    * 'destination' : (optional) path where to link the resource. This path
-    * 'placement' : (optional) gives the possibility to fine tune how the resource is linked into the main package stage
+    must be relative to the main package stage area.
-    area.
+    * 'placement' : (optional) gives the possibility to fine tune how the
+    resource is linked into the main package stage area.
     """
     when = kwargs.get('when', pkg.name)
     destination = kwargs.get('destination', "")
     placement = kwargs.get('placement', None)
     # Check if the path is relative
     if os.path.isabs(destination):
-        message = "The destination keyword of a resource directive can't be an absolute path.\n"
+        message = "The destination keyword of a resource directive can't be"
+        " an absolute path.\n"
         message += "\tdestination : '{dest}\n'".format(dest=destination)
         raise RuntimeError(message)
     # Check if the path falls within the main package stage area
-    test_path = 'stage_folder_root/'
+    test_path = 'stage_folder_root'
-    normalized_destination = os.path.normpath(join_path(test_path, destination))  # Normalized absolute path
+    normalized_destination = os.path.normpath(join_path(test_path, destination)
+                                              )  # Normalized absolute path
     if test_path not in normalized_destination:
-        message = "The destination folder of a resource must fall within the main package stage directory.\n"
+        message = "The destination folder of a resource must fall within the"
+        " main package stage directory.\n"
         message += "\tdestination : '{dest}'\n".format(dest=destination)
         raise RuntimeError(message)
     when_spec = parse_anonymous_spec(when, pkg.name)
@@ -307,6 +312,7 @@ def resource(pkg, **kwargs):
 
 class DirectiveError(spack.error.SpackError):
     """This is raised when something is wrong with a package directive."""
+
     def __init__(self, directive, message):
         super(DirectiveError, self).__init__(message)
         self.directive = directive
@@ -314,6 +320,7 @@ def __init__(self, directive, message):
 
 class CircularReferenceError(DirectiveError):
     """This is raised when something depends on itself."""
+
     def __init__(self, directive, package):
         super(CircularReferenceError, self).__init__(
             directive,

lib/spack/spack/directory_layout.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import re
 import os

lib/spack/spack/environment.py

@@ -1,7 +1,31 @@
-import os
+##############################################################################
-import os.path
+# 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 collections
 import inspect
+import os
+import os.path
 
 
 class NameModifier(object):
@@ -15,7 +39,8 @@ class NameValueModifier(object):
     def __init__(self, name, value, **kwargs):
         self.name = name
         self.value = value
-        self.args = {'name': name, 'value': value}
+        self.separator = kwargs.get('separator', ':')
+        self.args = {'name': name, 'value': value, 'delim': self.separator}
         self.args.update(kwargs)
 
 
@@ -26,44 +51,50 @@ def execute(self):
 
 class UnsetEnv(NameModifier):
     def execute(self):
-        os.environ.pop(self.name, None)  # Avoid throwing if the variable was not set
+        # Avoid throwing if the variable was not set
+        os.environ.pop(self.name, None)
 
 
 class SetPath(NameValueModifier):
     def execute(self):
-        string_path = concatenate_paths(self.value)
+        string_path = concatenate_paths(self.value, separator=self.separator)
         os.environ[self.name] = string_path
 
 
 class AppendPath(NameValueModifier):
     def execute(self):
         environment_value = os.environ.get(self.name, '')
-        directories = environment_value.split(':') if environment_value else []
+        directories = environment_value.split(
+            self.separator) if environment_value else []
         directories.append(os.path.normpath(self.value))
-        os.environ[self.name] = ':'.join(directories)
+        os.environ[self.name] = self.separator.join(directories)
 
 
 class PrependPath(NameValueModifier):
     def execute(self):
         environment_value = os.environ.get(self.name, '')
-        directories = environment_value.split(':') if environment_value else []
+        directories = environment_value.split(
+            self.separator) if environment_value else []
         directories = [os.path.normpath(self.value)] + directories
-        os.environ[self.name] = ':'.join(directories)
+        os.environ[self.name] = self.separator.join(directories)
 
 
 class RemovePath(NameValueModifier):
     def execute(self):
         environment_value = os.environ.get(self.name, '')
-        directories = environment_value.split(':') if environment_value else []
+        directories = environment_value.split(
-        directories = [os.path.normpath(x) for x in directories if x != os.path.normpath(self.value)]
+            self.separator) if environment_value else []
-        os.environ[self.name] = ':'.join(directories)
+        directories = [os.path.normpath(x) for x in directories
+                       if x != os.path.normpath(self.value)]
+        os.environ[self.name] = self.separator.join(directories)
 
 
 class EnvironmentModifications(object):
     """
     Keeps track of requests to modify the current environment.
 
-    Each call to a method to modify the environment stores the extra information on the caller in the request:
+    Each call to a method to modify the environment stores the extra
+    information on the caller in the request:
     - 'filename' : filename of the module where the caller is defined
     - 'lineno': line number where the request occurred
     - 'context' : line of code that issued the request that failed
@@ -71,10 +102,10 @@ class EnvironmentModifications(object):
 
     def __init__(self, other=None):
         """
-        Initializes a new instance, copying commands from other if it is not None
+        Initializes a new instance, copying commands from other if not None
 
         Args:
-            other: another instance of EnvironmentModifications from which (optional)
+            other: another instance of EnvironmentModifications (optional)
         """
         self.env_modifications = []
         if other is not None:
@@ -93,7 +124,8 @@ def extend(self, other):
     @staticmethod
     def _check_other(other):
         if not isinstance(other, EnvironmentModifications):
-            raise TypeError('other must be an instance of EnvironmentModifications')
+            raise TypeError(
+                'other must be an instance of EnvironmentModifications')
 
     def _get_outside_caller_attributes(self):
         stack = inspect.stack()
@@ -101,12 +133,10 @@ def _get_outside_caller_attributes(self):
             _, filename, lineno, _, context, index = stack[2]
             context = context[index].strip()
         except Exception:
-            filename, lineno, context = 'unknown file', 'unknown line', 'unknown context'
+            filename = 'unknown file'
-        args = {
+            lineno = 'unknown line'
-            'filename': filename,
+            context = 'unknown context'
-            'lineno': lineno,
+        args = {'filename': filename, 'lineno': lineno, 'context': context}
-            'context': context
-        }
         return args
 
     def set(self, name, value, **kwargs):
@@ -170,7 +200,8 @@ def prepend_path(self, name, path, **kwargs):
 
     def remove_path(self, name, path, **kwargs):
         """
-        Stores in the current object a request to remove a path from a path list
+        Stores in the current object a request to remove a path from a path
+        list
 
         Args:
             name: name of the path list in the environment
@@ -185,7 +216,8 @@ def group_by_name(self):
         Returns a dict of the modifications grouped by variable name
 
         Returns:
-            dict mapping the environment variable name to the modifications to be done on it
+            dict mapping the environment variable name to the modifications to
+            be done on it
         """
         modifications = collections.defaultdict(list)
         for item in self:
@@ -203,34 +235,39 @@ def apply_modifications(self):
         Applies the modifications and clears the list
         """
         modifications = self.group_by_name()
-        # Apply the modifications to the environment variables one variable at a time
+        # Apply modifications one variable at a time
         for name, actions in sorted(modifications.items()):
             for x in actions:
                 x.execute()
 
 
-def concatenate_paths(paths):
+def concatenate_paths(paths, separator=':'):
     """
-    Concatenates an iterable of paths into a  string of column separated paths
+    Concatenates an iterable of paths into a string of paths separated by
+    separator, defaulting to colon
 
     Args:
         paths: iterable of paths
+        separator: the separator to use, default ':'
 
     Returns:
         string
     """
-    return ':'.join(str(item) for item in paths)
+    return separator.join(str(item) for item in paths)
 
 
 def set_or_unset_not_first(variable, changes, errstream):
     """
-    Check if we are going to set or unset something after other modifications have already been requested
+    Check if we are going to set or unset something after other modifications
+    have already been requested
     """
-    indexes = [ii for ii, item in enumerate(changes) if ii != 0 and type(item) in [SetEnv, UnsetEnv]]
+    indexes = [ii for ii, item in enumerate(changes)
+               if ii != 0 and type(item) in [SetEnv, UnsetEnv]]
     if indexes:
         good = '\t    \t{context} at {filename}:{lineno}'
         nogood = '\t--->\t{context} at {filename}:{lineno}'
-        errstream('Suspicious requests to set or unset the variable \'{var}\' found'.format(var=variable))
+        message = 'Suspicious requests to set or unset the variable \'{var}\' found'  # NOQA: ignore=E501
+        errstream(message.format(var=variable))
         for ii, item in enumerate(changes):
             print_format = nogood if ii in indexes else good
             errstream(print_format.format(**item.args))
@@ -238,8 +275,8 @@ def set_or_unset_not_first(variable, changes, errstream):
 
 def validate(env, errstream):
     """
-    Validates the environment modifications to check for the presence of suspicious patterns. Prompts a warning for
+    Validates the environment modifications to check for the presence of
-    everything that was found
+    suspicious patterns. Prompts a warning for everything that was found
 
     Current checks:
     - set or unset variables after other changes on the same variable
@@ -250,3 +287,20 @@ def validate(env, errstream):
     modifications = env.group_by_name()
     for variable, list_of_changes in sorted(modifications.items()):
         set_or_unset_not_first(variable, list_of_changes, errstream)
+
+
+def filter_environment_blacklist(env, variables):
+    """
+    Generator that filters out any change to environment variables present in
+    the input list
+
+    Args:
+        env: list of environment modifications
+        variables: list of variable names to be filtered
+
+    Yields:
+        items in env if they are not in variables
+    """
+    for item in env:
+        if item.name not in variables:
+            yield item

lib/spack/spack/error.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
 import sys

lib/spack/spack/fetch_strategy.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
 Fetch strategies are used to download source code into a staging area
@@ -57,7 +57,6 @@
 from spack.util.compression import decompressor_for, extension
 
 import spack.util.pattern as pattern
-
 """List of all fetch strategies, created by FetchStrategy metaclass."""
 all_strategies = []
 
@@ -82,13 +81,16 @@ class FetchStrategy(object):
 
     class __metaclass__(type):
         """This metaclass registers all fetch strategies in a list."""
+
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
-            if cls.enabled: all_strategies.append(cls)
+            if cls.enabled:
+                all_strategies.append(cls)
 
     def __init__(self):
-        # The stage is initialized late, so that fetch strategies can be constructed
+        # The stage is initialized late, so that fetch strategies can be
-        # at package construction time.  This is where things will be fetched.
+        # constructed at package construction time.  This is where things
+        # will be fetched.
         self.stage = None
 
     def set_stage(self, stage):
@@ -97,15 +99,20 @@ def set_stage(self, stage):
         self.stage = stage
 
     # Subclasses need to implement these methods
-    def fetch(self):   pass  # Return True on success, False on fail.
+    def fetch(self):
+        pass  # Return True on success, False on fail.
 
-    def check(self):   pass  # Do checksum.
+    def check(self):
+        pass  # Do checksum.
 
-    def expand(self):  pass  # Expand archive.
+    def expand(self):
+        pass  # Expand archive.
 
-    def reset(self):   pass  # Revert to freshly downloaded state.
+    def reset(self):
+        pass  # Revert to freshly downloaded state.
 
-    def archive(self, destination): pass  # Used to create tarball for mirror.
+    def archive(self, destination):
+        pass  # Used to create tarball for mirror.
 
     def __str__(self):  # Should be human readable URL.
         return "FetchStrategy.__str___"
@@ -139,10 +146,12 @@ def __init__(self, url=None, digest=None, **kwargs):
         # If URL or digest are provided in the kwargs, then prefer
         # those values.
         self.url = kwargs.get('url', None)
-        if not self.url: self.url = url
+        if not self.url:
+            self.url = url
 
         self.digest = kwargs.get('md5', None)
-        if not self.digest: self.digest = digest
+        if not self.digest:
+            self.digest = digest
 
         self.expand_archive = kwargs.get('expand', True)
 
@@ -157,12 +166,30 @@ def fetch(self):
             tty.msg("Already downloaded %s" % self.archive_file)
             return
 
+        possible_files = self.stage.expected_archive_files
+        save_file = None
+        partial_file = None
+        if possible_files:
+            save_file = self.stage.expected_archive_files[0]
+            partial_file = self.stage.expected_archive_files[0] + '.part'
+
         tty.msg("Trying to fetch from %s" % self.url)
 
-        curl_args = ['-O',  # save file to disk
+        if partial_file:
+            save_args = ['-C',
+                         '-',  # continue partial downloads
+                         '-o',
+                         partial_file]  # use a .part file
+        else:
+            save_args = ['-O']
+
+        curl_args = save_args + [
             '-f',  # fail on >400 errors
-                     '-D', '-',  # print out HTML headers
+            '-D',
-                     '-L', self.url, ]
+            '-',  # print out HTML headers
+            '-L',  # resolve 3xx redirects
+            self.url,
+        ]
 
         if sys.stdout.isatty():
             curl_args.append('-#')  # status bar when using a tty
@@ -170,14 +197,16 @@ def fetch(self):
             curl_args.append('-sS')  # just errors when not.
 
         # Run curl but grab the mime type from the http headers
-        headers = spack.curl(
+        headers = spack.curl(*curl_args, output=str, fail_on_error=False)
-            *curl_args, output=str, fail_on_error=False)
 
         if spack.curl.returncode != 0:
             # clean up archive on failure.
             if self.archive_file:
                 os.remove(self.archive_file)
 
+            if partial_file and os.path.exists(partial_file):
+                os.remove(partial_file)
+
             if spack.curl.returncode == 22:
                 # This is a 404.  Curl will print the error.
                 raise FailedDownloadError(
@@ -188,27 +217,33 @@ def fetch(self):
                 raise FailedDownloadError(
                     self.url,
                     "Curl was unable to fetch due to invalid certificate. "
-                        "This is either an attack, or your cluster's SSL configuration "
+                    "This is either an attack, or your cluster's SSL "
-                        "is bad.  If you believe your SSL configuration is bad, you "
+                    "configuration is bad.  If you believe your SSL "
-                        "can try running spack -k, which will not check SSL certificates."
+                    "configuration is bad, you can try running spack -k, "
+                    "which will not check SSL certificates."
                     "Use this at your own risk.")
 
             else:
                 # This is some other curl error.  Curl will print the
                 # error, but print a spack message too
                 raise FailedDownloadError(
-                        self.url, "Curl failed with error %d" % spack.curl.returncode)
+                    self.url,
+                    "Curl failed with error %d" % spack.curl.returncode)
 
         # Check if we somehow got an HTML file rather than the archive we
         # asked for.  We only look at the last content type, to handle
         # 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.",
+            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.")
 
+        if save_file:
+            os.rename(partial_file, save_file)
+
         if not self.archive_file:
             raise FailedDownloadError(self.url)
 
@@ -227,14 +262,16 @@ def expand(self):
 
         self.stage.chdir()
         if not self.archive_file:
-            raise NoArchiveFileError("URLFetchStrategy couldn't find archive file",
+            raise NoArchiveFileError(
+                "URLFetchStrategy couldn't find archive file",
                 "Failed on expand() for URL %s" % self.url)
 
         decompress = decompressor_for(self.archive_file)
 
         # Expand all tarballs in their own directory to contain
         # exploding tarballs.
-        tarball_container = os.path.join(self.stage.path, "spack-expanded-archive")
+        tarball_container = os.path.join(self.stage.path,
+                                         "spack-expanded-archive")
         mkdirp(tarball_container)
         os.chdir(tarball_container)
         decompress(self.archive_file)
@@ -275,19 +312,24 @@ def check(self):
         """Check the downloaded archive against a checksum digest.
            No-op if this stage checks code out of a repository."""
         if not self.digest:
-            raise NoDigestError("Attempt to check URLFetchStrategy with no digest.")
+            raise NoDigestError(
+                "Attempt to check URLFetchStrategy with no digest.")
 
         checker = crypto.Checker(self.digest)
         if not checker.check(self.archive_file):
             raise ChecksumError(
-                    "%s checksum failed for %s" % (checker.hash_name, self.archive_file),
+                "%s checksum failed for %s" %
+                (checker.hash_name, self.archive_file),
                 "Expected %s but got %s" % (self.digest, checker.sum))
 
     @_needs_stage
     def reset(self):
-        """Removes the source path if it exists, then re-expands the archive."""
+        """
+        Removes the source path if it exists, then re-expands the archive.
+        """
         if not self.archive_file:
-            raise NoArchiveFileError("Tried to reset URLFetchStrategy before fetching",
+            raise NoArchiveFileError(
+                "Tried to reset URLFetchStrategy before fetching",
                 "Failed on reset() for URL %s" % self.url)
 
         # Remove everythigng but the archive from the stage
@@ -317,14 +359,16 @@ def __init__(self, name, *rev_types, **kwargs):
 
         # Set a URL based on the type of fetch strategy.
         self.url = kwargs.get(name, None)
-        if not self.url: raise ValueError(
+        if not self.url:
+            raise ValueError(
                 "%s requires %s argument." % (self.__class__, name))
 
         # Ensure that there's only one of the rev_types
         if sum(k in kwargs for k in rev_types) > 1:
             raise FetchStrategyError(
                 "Supply only one of %s to fetch with %s" % (
-                        comma_or(rev_types), name))
+                    comma_or(rev_types), name
+                ))
 
         # Set attributes for each rev type.
         for rt in rev_types:
@@ -362,8 +406,68 @@ def __repr__(self):
         return "%s<%s>" % (self.__class__, self.url)
 
 
+class GoFetchStrategy(VCSFetchStrategy):
+    """
+    Fetch strategy that employs the `go get` infrastructure
+    Use like this in a package:
+
+       version('name',
+               go='github.com/monochromegane/the_platinum_searcher/...')
+
+    Go get does not natively support versions, they can be faked with git
+    """
+    enabled = True
+    required_attributes = ('go', )
+
+    def __init__(self, **kwargs):
+        # Discards the keywords in kwargs that may conflict with the next
+        # call to __init__
+        forwarded_args = copy.copy(kwargs)
+        forwarded_args.pop('name', None)
+
+        super(GoFetchStrategy, self).__init__('go', **forwarded_args)
+        self._go = None
+
+    @property
+    def go_version(self):
+        vstring = self.go('version', output=str).split(' ')[2]
+        return Version(vstring)
+
+    @property
+    def go(self):
+        if not self._go:
+            self._go = which('go', required=True)
+        return self._go
+
+    @_needs_stage
+    def fetch(self):
+        self.stage.chdir()
+
+        tty.msg("Trying to get go resource:", self.url)
+
+        try:
+            os.mkdir('go')
+        except OSError:
+            pass
+        env = dict(os.environ)
+        env['GOPATH'] = os.path.join(os.getcwd(), 'go')
+        self.go('get', '-v', '-d', self.url, env=env)
+
+    def archive(self, destination):
+        super(GoFetchStrategy, self).archive(destination, exclude='.git')
+
+    @_needs_stage
+    def reset(self):
+        self.stage.chdir_to_source()
+        self.go('clean')
+
+    def __str__(self):
+        return "[go] %s" % self.url
+
+
 class GitFetchStrategy(VCSFetchStrategy):
-    """Fetch strategy that gets source code from a git repository.
+    """
+    Fetch strategy that gets source code from a git repository.
     Use like this in a package:
 
         version('name', git='https://github.com/project/repo.git')
@@ -379,10 +483,11 @@ class GitFetchStrategy(VCSFetchStrategy):
         * ``commit``: Particular commit hash in the repo
     """
     enabled = True
-    required_attributes = ('git',)
+    required_attributes = ('git', )
 
     def __init__(self, **kwargs):
-        # Discards the keywords in kwargs that may conflict with the next call to __init__
+        # Discards the keywords in kwargs that may conflict with the next call
+        # to __init__
         forwarded_args = copy.copy(kwargs)
         forwarded_args.pop('name', None)
 
@@ -495,7 +600,8 @@ class SvnFetchStrategy(VCSFetchStrategy):
     required_attributes = ['svn']
 
     def __init__(self, **kwargs):
-        # Discards the keywords in kwargs that may conflict with the next call to __init__
+        # Discards the keywords in kwargs that may conflict with the next call
+        # to __init__
         forwarded_args = copy.copy(kwargs)
         forwarded_args.pop('name', None)
 
@@ -556,14 +662,16 @@ def __str__(self):
 
 
 class HgFetchStrategy(VCSFetchStrategy):
-    """Fetch strategy that gets source code from a Mercurial repository.
+    """
+    Fetch strategy that gets source code from a Mercurial repository.
     Use like this in a package:
 
         version('name', hg='https://jay.grs.rwth-aachen.de/hg/lwm2')
 
     Optionally, you can provide a branch, or revision to check out, e.g.:
 
-           version('torus', hg='https://jay.grs.rwth-aachen.de/hg/lwm2', branch='torus')
+        version('torus',
+                hg='https://jay.grs.rwth-aachen.de/hg/lwm2', branch='torus')
 
     You can use the optional 'revision' attribute to check out a
     branch, tag, or particular revision in hg.  To prevent
@@ -576,7 +684,8 @@ class HgFetchStrategy(VCSFetchStrategy):
     required_attributes = ['hg']
 
     def __init__(self, **kwargs):
-        # Discards the keywords in kwargs that may conflict with the next call to __init__
+        # Discards the keywords in kwargs that may conflict with the next call
+        # to __init__
         forwarded_args = copy.copy(kwargs)
         forwarded_args.pop('name', None)
 
@@ -655,7 +764,8 @@ def from_kwargs(**kwargs):
             return fetcher(**kwargs)
     # Raise an error in case we can't instantiate any known strategy
     message = "Cannot instantiate any FetchStrategy"
-    long_message = message + " from the given arguments : {arguments}".format(srguments=kwargs)
+    long_message = message + " from the given arguments : {arguments}".format(
+        srguments=kwargs)
     raise FetchError(message, long_message)
 
 
@@ -667,7 +777,7 @@ def for_package_version(pkg, version):
     """Determine a fetch strategy based on the arguments supplied to
        version() in the package description."""
     # If it's not a known version, extrapolate one.
-    if not version in pkg.versions:
+    if version not in pkg.versions:
         url = pkg.url_for_version(version)
         if not url:
             raise InvalidArgsError(pkg, version)
@@ -735,7 +845,8 @@ def __init__(self, msg, long_msg=None):
 
 class InvalidArgsError(FetchError):
     def __init__(self, pkg, version):
-        msg = "Could not construct a fetch strategy for package %s at version %s"
+        msg = ("Could not construct a fetch strategy for package %s at "
+               "version %s")
         msg %= (pkg.name, version)
         super(InvalidArgsError, self).__init__(msg)
 
@@ -752,4 +863,5 @@ class NoStageError(FetchError):
 
     def __init__(self, method):
         super(NoStageError, self).__init__(
-                "Must call FetchStrategy.set_stage() before calling %s" % method.__name__)
+            "Must call FetchStrategy.set_stage() before calling %s" %
+            method.__name__)

lib/spack/spack/graph.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """Functions for graphing DAGs of dependencies.
 

lib/spack/spack/hooks/__init__.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """This package contains modules with hooks for various stages in the
    Spack install process.  You can add modules here and they'll be

lib/spack/spack/hooks/dotkit.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import spack.modules
 

lib/spack/spack/hooks/extensions.py

@@ -1,26 +1,26 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# 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 General Public License (as published by
+# it under the terms of the GNU Lesser General Public License (as
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
+# You should have received a copy of the GNU Lesser General Public
-# along with this program; if not, write to the Free Software Foundation,
+# License along with this program; if not, write to the Free Software
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 
 import spack