Edits...

2. Beginning to write three methods of application developer support.  Two methods were moved from elsewhere.

.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 +1,23 @@
+# -*- 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 ‘,’
+#
+# Let people use terse Python features:
+# - E731 : lambda expressions
+#
+# 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 = E129,E221,E241,E272,E731,F403,F821,F999,F405
+max-line-length = 79

.gitignore

@@ -1,9 +1,17 @@
 /var/spack/stage
+/var/spack/cache
+/var/spack/repos/*/index.yaml
+/var/spack/repos/*/lock
 *.pyc
-/opt/
+/opt
 *~
 .DS_Store
 .idea
+/etc/spack/licenses
+/etc/spack/*.yaml
 /etc/spackconfig
 /share/spack/dotkit
 /share/spack/modules
+/TAGS
+/htmlcov
+.coverage

.mailmap

@@ -0,0 +1,20 @@
+Todd Gamblin       <tgamblin@llnl.gov>          George Todd Gamblin <gamblin2@llnl.gov>
+Todd Gamblin       <tgamblin@llnl.gov>          Todd Gamblin        <gamblin2@llnl.gov>
+Adam Moody         <moody20@llnl.gov>           Adam T. Moody       <moody20@llnl.gov>
+Alfredo Gimenez    <gimenez1@llnl.gov>          Alfredo Gimenez     <alfredo.gimenez@gmail.com>
+David Boehme       <boehme3@llnl.gov>           David Boehme        <boehme3@sierra324.llnl.gov>
+David Boehme       <boehme3@llnl.gov>           David Boehme        <boehme3@sierra648.llnl.gov>
+Kevin Brandstatter <kjbrandstatter@gmail.com>   Kevin Brandstatter  <kbrandst@hawk.iit.edu>
+Luc Jaulmes        <luc.jaulmes@bsc.es>         Luc Jaulmes         <jaulmes1@llnl.gov>
+Saravan Pantham    <saravan.pantham@gmail.com>  Saravan Pantham     <pantham1@surface86.llnl.gov>
+Tom Scogland       <tscogland@llnl.gov>         Tom Scogland        <scogland1@llnl.gov>
+Tom Scogland       <tscogland@llnl.gov>         Tom Scogland        <tom.scogland@gmail.com>
+Joachim Protze     <protze@rz.rwth-aachen.de>   jprotze             <protze@rz.rwth-aachen.de>
+Gregory L. Lee     <lee218@llnl.gov>            Gregory L. Lee      <lee218@surface86.llnl.gov>
+Gregory L. Lee     <lee218@llnl.gov>            Gregory L. Lee      <lee218@cab687.llnl.gov>
+Gregory L. Lee     <lee218@llnl.gov>            Gregory L. Lee      <lee218@cab690.llnl.gov>
+Gregory L. Lee     <lee218@llnl.gov>            Gregory L. Lee      <lee218@catalyst159.llnl.gov>
+Gregory L. Lee     <lee218@llnl.gov>            Gregory Lee         <lee218@llnl.gov>
+Massimiliano Culpo <massimiliano.culpo@epfl.ch> Massimiliano Culpo  <massimiliano.culpo@googlemail.com>
+Massimiliano Culpo <massimiliano.culpo@epfl.ch> alalazo             <massimiliano.culpo@googlemail.com>
+Mark Miller        <miller86@llnl.gov>          miller86            <miller86@llnl.gov>

.travis.yml

@@ -0,0 +1,46 @@
+language: python
+
+python:
+  - "2.6"
+  - "2.7"
+env:
+  - TEST_TYPE=unit
+  - TEST_TYPE=flake8
+
+# Exclude flake8 from python 2.6
+matrix:
+  exclude:
+  - python: "2.6"
+    env: TEST_TYPE=flake8
+
+# Use new Travis infrastructure (Docker can't sudo yet)
+sudo: false
+
+# Install coveralls to obtain code coverage
+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:
+  # Run unit tests with code coverage plus install libdwarf
+  - 'if [ "$TEST_TYPE" = "unit" ]; then share/spack/qa/run-unit-tests; fi'
+  # Run flake8 code style checks.
+  - 'if [ "$TEST_TYPE" = "flake8" ]; then share/spack/qa/run-flake8; fi'
+
+after_success:
+  - 'if [ "$TEST_TYPE" = "unit" ] && [ "$TRAVIS_PYTHON_VERSION" = "2.7" ]; then coveralls; fi'
+
+notifications:
+  email:
+    recipients:
+      - tgamblin@llnl.gov
+    on_success: change
+    on_failure: always

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://scalability-llnl.github.io/spack
+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
-the Free Software Foundation) version 2.1 dated February 1999.
+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 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
-along with this program; if not, write to the Free Software Foundation,
-Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+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
 
-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
-U.S. Department of Energy (DOE). This work was produced at the
-Lawrence Livermore National Laboratory under Contract
-No. DE-AC52-07NA27344 with the DOE.
+A. This notice is required to be provided under LLNL's contract with
+   the U.S. Department of Energy (DOE). This work was produced at the
+   Lawrence Livermore National Laboratory under Contract
+   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,
-express or implied, or assumes any liability or responsibility for the
-accuracy, completeness, or usefulness of any information, apparatus,
-product, or process disclosed, or represents that its use would not
-infringe privately-owned rights.
+   National Security, LLC nor any of their employees, makes any
+   warranty, express or implied, or assumes any liability or
+   responsibility for the accuracy, completeness, or usefulness of any
+   information, apparatus, product, or process disclosed, or
+   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
-otherwise does not necessarily constitute or imply its endorsement,
-recommendation, or favoring by the United States Government or
-Lawrence Livermore National Security, LLC. The views and opinions of
-authors expressed herein do not necessarily state or reflect those of
-the United States Government or Lawrence Livermore National Security,
-LLC, and shall not be used for advertising or product endorsement
-purposes.
+   process, or services by trade name, trademark, manufacturer or
+   otherwise does not necessarily constitute or imply its endorsement,
+   recommendation, or favoring by the United States Government or
+   Lawrence Livermore National Security, LLC. The views and opinions
+   of authors expressed herein do not necessarily state or reflect
+   those of the United States Government or Lawrence Livermore
+   National Security, LLC, and shall not be used for advertising or
+   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

@@ -1,5 +1,8 @@
-Spack
-===========
+![image](share/spack/logo/spack-logo-text-64.png "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
@@ -13,42 +16,86 @@ can coexist on the same system.
 Most importantly, Spack is simple. It offers a simple spec syntax so
 that users can specify versions and configuration options
 concisely. Spack is also simple for package authors: package files are
-writtin in pure Python, and specs allow package authors to write a
+written in pure Python, and specs allow package authors to write a
 single build script for many different builds of the same package.
 
 See the
-[Feature Overview](http://scalability-llnl.github.io/spack/features.html)
+[Feature Overview](http://software.llnl.gov/spack/features.html)
 for examples and highlights.
 
 To install spack and install your first package:
 
-    $ git clone https://github.com/scalability-llnl/spack.git
+    $ git clone https://github.com/llnl/spack.git
     $ cd spack/bin
     $ ./spack install libelf
 
 Documentation
 ----------------
 
-[Full documentation](http://scalability-llnl.github.io/spack)
-for Spack is also available.
+[**Full documentation**](http://software.llnl.gov/spack) for Spack is
+the first place to look.
+
+See also:
+  * [Technical paper](http://www.computer.org/csdl/proceedings/sc/2015/3723/00/2807623.pdf) and
+    [slides](https://tgamblin.github.io/files/Gamblin-Spack-SC15-Talk.pdf) on Spack's design and implementation.
+  * [Short presentation](https://tgamblin.github.io/files/Gamblin-Spack-Lightning-Talk-BOF-SC15.pdf) from the *Getting Scientific Software Installed* BOF session at Supercomputing 2015.
+
+
+Get Involved!
+------------------------
+
+Spack is an open source project.  Questions, discussion, and
+contributions are welcome. Contributions can be anything from new
+packages to bugfixes, or even new core features.
+
+### Mailing list
+
+If you are interested in contributing to spack, the first step is to
+join the mailing list.  We're using a Google Group for this, and you
+can join it here:
+
+  * [Spack Google Group](https://groups.google.com/d/forum/spack)
+
+### Contributions
+
+Contributing to Spack is relatively easy.  Just send us 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).
+
+Before you send a PR, your code should pass the following checks:
+
+* Your contribution will need to pass the `spack test` command.
+  Run this before submitting your PR.
+
+* Also run the `share/spack/qa/run-flake8` script to check for PEP8 compliance.
+  To encourage contributions and readability by a broad audience,
+  Spack uses the [PEP8](https://www.python.org/dev/peps/pep-0008/) coding
+  standard with [a few exceptions](https://github.com/LLNL/spack/blob/develop/.flake8).
+
+We enforce these guidelines with [Travis CI](https://travis-ci.org/LLNL/spack).
+
+Spack uses a rough approximation of the [Git
+Flow](http://nvie.com/posts/a-successful-git-branching-model/)
+branching model.  The ``develop`` branch contains the latest
+contributions, and ``master`` is always tagged and points to the
+latest stable release.
+
 
 Authors
 ----------------
-Spack was written by Todd Gamblin, tgamblin@llnl.gov.
+Many thanks go to Spack's [contributors](https://github.com/llnl/spack/graphs/contributors).
 
-Significant contributions were also made by:
+Spack was originally written by Todd Gamblin, tgamblin@llnl.gov.
 
-  * David Beckingsale
-  * David Boehme
-  * Alfredo Gimenez
-  * Luc Jaulmes
-  * Matt Legendre
-  * Greg Lee
-  * Adam Moody
-  * Saravan Pantham
-  * Joachim Protze
-  * Bob Robey
-  * Justin Too
+### Citing Spack
+
+If you are referencing Spack in a publication, please cite the following paper:
+
+ * Todd Gamblin, Matthew P. LeGendre, Michael R. Collette, Gregory L. Lee,
+   Adam Moody, Bronis R. de Supinski, and W. Scott Futral.
+   [**The Spack Package Manager: Bringing Order to HPC Software Chaos**](http://www.computer.org/csdl/proceedings/sc/2015/3723/00/2807623.pdf).
+   In *Supercomputing 2015 (SC’15)*, Austin, Texas, November 15-20 2015. LLNL-CONF-669890.
 
 Release
 ----------------

bin/sbang

@@ -0,0 +1,119 @@
+#!/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.
+#
+# Many operating systems limit the length of shebang lines, making it
+# hard to use interpreters that are deep in the directory hierarchy.
+# `sbang` can run such scripts, either as a shebang interpreter, or
+# directly on the command line.
+#
+# Usage
+# -----------------------------
+# Suppose you have a script, long-shebang.sh, like this:
+#
+#     1    #!/very/long/path/to/some/interpreter
+#     2
+#     3    echo "success!"
+#
+# Invoking this script will result in an error on some OS's.  On
+# Linux, you get this:
+#
+#     $ ./long-shebang.sh
+#     -bash: ./long: /very/long/path/to/some/interp: bad interpreter:
+#            No such file or directory
+#
+# On Mac OS X, the system simply assumes the interpreter is the shell
+# and tries to run with it, which is likely not what you want.
+#
+#
+# `sbang` on the command line
+# -----------------------------
+# You can use `sbang` in two ways.  The first is to use it directly,
+# from the command line, like this:
+#
+#     $ sbang ./long-shebang.sh
+#     success!
+#
+#
+# `sbang` as the interpreter
+# -----------------------------
+# You can also use `sbang` *as* the interpreter for your script. Put
+# `#!/bin/bash /path/to/sbang` on line 1, and move the original
+# shebang to line 2 of the script:
+#
+#     1    #!/bin/bash /path/to/sbang
+#     2    #!/long/path/to/real/interpreter with arguments
+#     3
+#     4    echo "success!"
+#
+#     $ ./long-shebang.sh
+#     success!
+#
+# On Linux, you could shorten line 1 to `#!/path/to/sbang`, but other
+# operating systems like Mac OS X require the interpreter to be a
+# binary, so it's best to use `sbang` as a `bash` argument.
+# Obviously, for this to work, `sbang` needs to have a short enough
+# path that *it* will run without hitting OS limits.
+#
+# For Lua, scripts the second line can't start with #!, as # is not
+# the comment character in lua (even though lua ignores #! on the
+# *first* line of a script).  So, instrument a lua script like this,
+# using -- instead of # on the second line:
+#
+#     1    #!/bin/bash /path/to/sbang
+#     2    --!/long/path/to/lua with arguments
+#     3
+#     4    print "success!"
+#
+# How it works
+# -----------------------------
+# `sbang` is a very simple bash script. It looks at the first two
+# lines of a script argument and runs the last line starting with
+# `#!`, with the script as an argument. It also forwards arguments.
+#
+
+# First argument is the script we want to actually run.
+script="$1"
+
+# Search the first two lines of script for interpreters.
+lines=0
+while read line && ((lines < 2)) ; do
+    if [[ "$line" = '#!'* ]]; then
+        interpreter="${line#\#!}"
+    elif [[ "$line" = '--!'*lua* ]]; then
+        interpreter="${line#--!}"
+    fi
+    lines=$((lines+1))
+done < "$script"
+
+# Invoke any interpreter found, or raise an error if none was found.
+if [ -n "$interpreter" ]; then
+    exec $interpreter "$@"
+else
+    echo "error: sbang found no interpreter in $script"
+    exit 1
+fi

bin/spack

@@ -1,32 +1,34 @@
 #!/usr/bin/env python
+# flake8: noqa
 ##############################################################################
-# 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://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
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 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
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
-if not sys.version_info[:2] >= (2,6):
+if not sys.version_info[:2] >= (2, 6):
     v_info = sys.version_info[:3]
-    sys.exit("Spack requires Python 2.6 or higher.  This is Python %d.%d.%d." % v_info)
+    sys.exit("Spack requires Python 2.6 or higher. "
+             "This is Python %d.%d.%d." % v_info)
 
 import os
 
@@ -38,6 +40,32 @@ SPACK_PREFIX = os.path.dirname(os.path.dirname(SPACK_FILE))
 # Allow spack libs to be imported in our scripts
 SPACK_LIB_PATH = os.path.join(SPACK_PREFIX, "lib", "spack")
 sys.path.insert(0, SPACK_LIB_PATH)
+SPACK_EXTERNAL_LIBS = os.path.join(SPACK_LIB_PATH, "external")
+sys.path.insert(0, SPACK_EXTERNAL_LIBS)
+
+import warnings
+# Avoid warnings when nose is installed with the python exe being used to run
+# spack. Note this must be done after Spack's external libs directory is added
+# to sys.path.
+with warnings.catch_warnings():
+    warnings.filterwarnings("ignore", ".*nose was already imported")
+    import nose
+
+# Quick and dirty check to clean orphaned .pyc files left over from
+# previous revisions.  These files were present in earlier versions of
+# Spack, were removed, but shadow system modules that Spack still
+# imports.  If we leave them, Spack will fail in mysterious ways.
+# TODO: more elegant solution for orphaned pyc files.
+orphaned_pyc_files = [os.path.join(SPACK_EXTERNAL_LIBS, n)
+                      for n in ('functools.pyc', 'ordereddict.pyc')]
+for pyc_file in orphaned_pyc_files:
+    if not os.path.exists(pyc_file):
+        continue
+    try:
+        os.remove(pyc_file)
+    except OSError as e:
+        print ("WARNING: Spack may fail mysteriously. "
+               "Couldn't remove orphaned .pyc file: %s" % pyc_file)
 
 # If there is no working directory, use the spack prefix.
 try:
@@ -49,25 +77,41 @@ except OSError:
 # clean up the scope and start using spack package instead.
 del SPACK_FILE, SPACK_PREFIX, SPACK_LIB_PATH
 import llnl.util.tty as tty
+from llnl.util.tty.color import *
 import spack
 from spack.error import SpackError
-from external import argparse
+import argparse
 
 # Command parsing
 parser = argparse.ArgumentParser(
-    description='Spack: the Supercomputing PACKage Manager.')
-parser.add_argument('-V', '--version', action='version',
-                    version="%s" % spack.spack_version)
-parser.add_argument('-v', '--verbose', action='store_true',
-                    help="Print additional output during builds")
+    formatter_class=argparse.RawTextHelpFormatter,
+    description="Spack: the Supercomputing PACKage Manager." + colorize("""
+
+spec expressions:
+  PACKAGE [CONSTRAINTS]
+
+    CONSTRAINTS:
+      @c{@version}
+      @g{%compiler  @compiler_version}
+      @B{+variant}
+      @r{-variant} or @r{~variant}
+      @m{=architecture}
+      [^DEPENDENCY [CONSTRAINTS] ...]"""))
+
 parser.add_argument('-d', '--debug', action='store_true',
                     help="Write out debug logs during compile")
+parser.add_argument('-D', '--pdb', action='store_true',
+                    help="Run spack under the pdb debugger")
 parser.add_argument('-k', '--insecure', action='store_true',
-                    help="Do not check ssl certificates when downloading archives.")
+                    help="Do not check ssl certificates when downloading.")
 parser.add_argument('-m', '--mock', action='store_true',
                     help="Use mock packages instead of real ones.")
 parser.add_argument('-p', '--profile', action='store_true',
                     help="Profile execution using cProfile.")
+parser.add_argument('-v', '--verbose', action='store_true',
+                    help="Print additional output during builds")
+parser.add_argument('-V', '--version', action='version',
+                    version="%s" % spack.spack_version)
 
 # each command module implements a parser() function, to which we pass its
 # subparser for setup.
@@ -87,49 +131,54 @@ if len(sys.argv) == 1:
 # actually parse the args.
 args = parser.parse_args()
 
+
 def main():
     # Set up environment based on args.
     tty.set_verbose(args.verbose)
     tty.set_debug(args.debug)
     spack.debug = args.debug
 
+    if spack.debug:
+        import spack.util.debug as debug
+        debug.register_interrupt_handler()
+
+    from spack.yaml_version_check import check_yaml_versions
+    check_yaml_versions()
+
     spack.spack_working_dir = working_dir
     if args.mock:
-        from spack.packages import PackageDB
-        spack.db = PackageDB(spack.mock_packages_path)
+        from spack.repository import RepoPath
+        spack.repo.swap(RepoPath(spack.mock_packages_path))
 
     # If the user asked for it, don't check ssl certs.
     if args.insecure:
-        tty.warn("You asked for --insecure, which does not check SSL certificates or checksums.")
+        tty.warn("You asked for --insecure. Will NOT check SSL certificates.")
         spack.curl.add_default_arg('-k')
 
     # Try to load the particular command asked for and run it
     command = spack.cmd.get_command(args.command)
     try:
         return_val = command(parser, args)
-    except SpackError, e:
-        if spack.debug:
-            # In debug mode, raise with a full stack trace.
-            raise
-        elif e.long_message:
-            tty.die(e.message, e.long_message)
-        else:
-            tty.die(e.message)
-
+    except SpackError as e:
+        e.die()
     except KeyboardInterrupt:
         sys.stderr.write('\n')
         tty.die("Keyboard interrupt.")
 
-    # Allow commands to return values if they want to exit with some ohter code.
+    # Allow commands to return values if they want to exit with some other code.
     if return_val is None:
         sys.exit(0)
     elif isinstance(return_val, int):
         sys.exit(return_val)
     else:
-        tty.die("Bad return value from command %s: %s" % (args.command, return_val))
+        tty.die("Bad return value from command %s: %s"
+                % (args.command, return_val))
 
 if args.profile:
     import cProfile
-    cProfile.run('main()', sort='tottime')
+    cProfile.run('main()', sort='time')
+elif args.pdb:
+    import pdb
+    pdb.run('main()')
 else:
     main()

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://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
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 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
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# 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
 ##############################################################################
 #
 # spack-python

etc/spack/defaults/modules.yaml

@@ -0,0 +1,40 @@
+# -------------------------------------------------------------------------
+# This is the default configuration for Spack's module file generation.
+#
+# Settings here are versioned with Spack and are intended to provide
+# sensible defaults out of the box. Spack maintainers should edit this
+# file to keep it current.
+#
+# Users can override these settings by editing the following files.
+#
+# Per-spack-instance settings (overrides defaults):
+#   $SPACK_ROOT/etc/spack/modules.yaml
+#
+# Per-user settings (overrides default and site settings):
+#   ~/.spack/modules.yaml
+# -------------------------------------------------------------------------
+modules:
+  enable:
+    - tcl
+    - dotkit
+  prefix_inspections:
+    bin:
+      - PATH
+    man:
+      - MANPATH
+    share/man:
+      - MANPATH
+    lib:
+      - LIBRARY_PATH
+      - LD_LIBRARY_PATH
+    lib64:
+      - LIBRARY_PATH
+      - LD_LIBRARY_PATH
+    include:
+      - CPATH
+    lib/pkgconfig:
+      - PKG_CONFIG_PATH
+    lib64/pkgconfig:
+      - PKG_CONFIG_PATH
+    '':
+      - CMAKE_PREFIX_PATH

etc/spack/defaults/packages.yaml

@@ -0,0 +1,21 @@
+# -------------------------------------------------------------------------
+# This file controls default concretization preferences for Spack.
+#
+# Settings here are versioned with Spack and are intended to provide
+# sensible defaults out of the box. Spack maintainers should edit this
+# file to keep it current.
+#
+# Users can override these settings by editing the following files.
+#
+# Per-spack-instance settings (overrides defaults):
+#   $SPACK_ROOT/etc/spack/packages.yaml
+#
+# Per-user settings (overrides default and site settings):
+#   ~/.spack/packages.yaml
+# -------------------------------------------------------------------------
+packages:
+  all:
+    providers:
+      mpi: [openmpi, mpich]
+      blas: [openblas]
+      lapack: [openblas]

etc/spack/defaults/repos.yaml

@@ -0,0 +1,14 @@
+# -------------------------------------------------------------------------
+# This is the default spack repository configuration. It includes the
+# builtin spack package repository.
+#
+# Users can override these settings by editing the following files.
+#
+# Per-spack-instance settings (overrides defaults):
+#   $SPACK_ROOT/etc/spack/repos.yaml
+#
+# Per-user settings (overrides default and site settings):
+#   ~/.spack/repos.yaml
+# -------------------------------------------------------------------------
+repos:
+  - $spack/var/spack/repos/builtin

lib/spack/docs/_themes/sphinx_rtd_theme/__init__.py

@@ -5,7 +5,7 @@
 """
 import os
 
-VERSION = (0, 1, 5)
+VERSION = (0, 1, 8)
 
 __version__ = ".".join(str(v) for v in VERSION)
 __version_full__ = __version__

lib/spack/docs/_themes/sphinx_rtd_theme/breadcrumbs.html

@@ -1,15 +1,23 @@
-<ul class="wy-breadcrumbs">
-  <li><a href="{{ pathto(master_doc) }}">Docs</a> &raquo;</li>
-  <li><a href="">{{ title }}</a></li>
-    <li class="wy-breadcrumbs-aside">
-      {% if display_github %}
-        <a href="https://github.com/{{ github_user }}/{{ github_repo }}/blob/{{ github_version }}{{ conf_py_path }}{{ pagename }}.rst" class="icon icon-github"> Edit on GitHub</a>
-      {% elif display_bitbucket %}
-        <a href="https://bitbucket.org/{{ bitbucket_user }}/{{ bitbucket_repo }}/src/{{ bitbucket_version}}{{ conf_py_path }}{{ pagename }}.rst'" class="icon icon-bitbucket"> Edit on Bitbucket</a>
-      {% elif show_source and has_source and sourcename %}
-        <a href="{{ pathto('_sources/' + sourcename, true)|e }}" rel="nofollow"> View page source</a>
-      {% endif %}
-    </li>
-</ul>
-<hr/>
-
+<div role="navigation" aria-label="breadcrumbs navigation">
+  <ul class="wy-breadcrumbs">
+    <li><a href="{{ pathto(master_doc) }}">Docs</a> &raquo;</li>
+      {% for doc in parents %}
+          <li><a href="{{ doc.link|e }}">{{ doc.title }}</a> &raquo;</li>
+      {% endfor %}
+    <li>{{ title }}</li>
+      <li class="wy-breadcrumbs-aside">
+        {% if pagename != "search" %}
+          {% if display_github %}
+            <a href="https://{{ github_host|default("github.com") }}/{{ github_user }}/{{ github_repo }}/blob/{{ github_version }}{{ conf_py_path }}{{ pagename }}{{ source_suffix }}" class="fa fa-github"> Edit on GitHub</a>
+          {% elif display_bitbucket %}
+            <a href="https://bitbucket.org/{{ bitbucket_user }}/{{ bitbucket_repo }}/src/{{ bitbucket_version}}{{ conf_py_path }}{{ pagename }}{{ source_suffix }}" class="fa fa-bitbucket"> Edit on Bitbucket</a>
+          {% elif show_source and source_url_prefix %}
+            <a href="{{ source_url_prefix }}{{ pagename }}{{ source_suffix }}">View page source</a>
+          {% elif show_source and has_source and sourcename %}
+            <a href="{{ pathto('_sources/' + sourcename, true)|e }}" rel="nofollow"> View page source</a>
+          {% endif %}
+        {% endif %}
+      </li>
+  </ul>
+  <hr/>
+</div>

lib/spack/docs/_themes/sphinx_rtd_theme/footer.html

@@ -1,28 +1,40 @@
 <footer>
   {% if next or prev %}
-    <div class="rst-footer-buttons">
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
       {% if next %}
-        <a href="{{ next.link|e }}" class="btn btn-neutral float-right" title="{{ next.title|striptags|e }}"/>Next <span class="icon icon-circle-arrow-right"></span></a>
+        <a href="{{ next.link|e }}" class="btn btn-neutral float-right" title="{{ next.title|striptags|e }}" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
       {% endif %}
       {% if prev %}
-        <a href="{{ prev.link|e }}" class="btn btn-neutral" title="{{ prev.title|striptags|e }}"><span class="icon icon-circle-arrow-left"></span> Previous</a>
+        <a href="{{ prev.link|e }}" class="btn btn-neutral" title="{{ prev.title|striptags|e }}" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
       {% endif %}
     </div>
   {% endif %}
 
   <hr/>
 
-  <p>
-    &copy; Copyright 2013-2014,
-    <a href="https://scalability.llnl.gov/">Lawrence Livermore National Laboratory</a>.
-    <br/>
-    Written by Todd Gamblin, <a href="mailto:tgamblin@llnl.gov">tgamblin@llnl.gov</a>, LLNL-CODE-647188
-    <br/>
+  <div role="contentinfo">
+    <p>
+    {%- if show_copyright %}
+      {%- if hasdoc('copyright') %}
+        {% trans path=pathto('copyright'), copyright=copyright|e %}&copy; <a href="{{ path }}">Copyright</a> {{ copyright }}.{% endtrans %}
+      {%- else %}
+        {% trans copyright=copyright|e %}&copy; Copyright {{ copyright }}.{% endtrans %}
+      {%- endif %}
+    {%- endif %}
 
-  {%- if last_updated %}
-    {% trans last_updated=last_updated|e %}Last updated on {{ last_updated }}.{% endtrans %}
+    <br/>
+    Written by Todd Gamblin (<a href="mailto:tgamblin@llnl.gov">tgamblin@llnl.gov</a>) and
+    many contributors. LLNL-CODE-647188.
+
+    {%- if last_updated %}
+      <br/>
+      {% trans last_updated=last_updated|e %}Last updated on {{ last_updated }}.{% endtrans %}
+    {%- endif %}
+    </p>
+  </div>
+
+  {%- if show_sphinx %}
+  {% trans %}Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>{% endtrans %}.
   {%- endif %}
-  &nbsp;&nbsp;
-  {% trans %}<br/><a href="https://www.github.com/snide/sphinx_rtd_theme">Sphinx theme</a> provided by <a href="http://readthedocs.org">Read the Docs</a>{% endtrans %}
-  </p>
+
 </footer>

lib/spack/docs/_themes/sphinx_rtd_theme/layout.html

@@ -12,6 +12,7 @@
 <!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
 <head>
   <meta charset="utf-8">
+  {{ metatags }}
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   {% block htmltitle %}
   <title>{{ title|striptags|e }}{{ titlesuffix }}</title>
@@ -23,40 +24,28 @@
   {% endif %}
 
   {# CSS #}
-  <link href='https://fonts.googleapis.com/css?family=Lato:400,700|Roboto+Slab:400,700|Inconsolata:400,700' rel='stylesheet' type='text/css'>
 
-  {# JS #}
+  {# OPENSEARCH #}
   {% if not embedded %}
-
-    <script type="text/javascript">
-      var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:'{{ url_root }}',
-        VERSION:'{{ release|e }}',
-        COLLAPSE_INDEX:false,
-        FILE_SUFFIX:'{{ '' if no_search_suffix else file_suffix }}',
-        HAS_SOURCE:  {{ has_source|lower }}
-      };
-    </script>
-    {%- for scriptfile in script_files %}
-      <script type="text/javascript" src="{{ pathto(scriptfile, 1) }}"></script>
-    {%- endfor %}
-
     {% if use_opensearch %}
       <link rel="search" type="application/opensearchdescription+xml" title="{% trans docstitle=docstitle|e %}Search within {{ docstitle }}{% endtrans %}" href="{{ pathto('_static/opensearch.xml', 1) }}"/>
     {% endif %}
 
   {% endif %}
 
-  {# RTD hosts these file themselves, so just load on non RTD builds #}
+  {# RTD hosts this file, so just load on non RTD builds #}
   {% if not READTHEDOCS %}
     <link rel="stylesheet" href="{{ pathto('_static/' + style, 1) }}" type="text/css" />
-    <script type="text/javascript" src="_static/js/theme.js"></script>
   {% endif %}
 
   {% for cssfile in css_files %}
     <link rel="stylesheet" href="{{ pathto(cssfile, 1) }}" type="text/css" />
   {% endfor %}
 
+  {% for cssfile in extra_css_files %}
+    <link rel="stylesheet" href="{{ pathto(cssfile, 1) }}" type="text/css" />
+  {% endfor %}
+
   {%- block linktags %}
     {%- if hasdoc('about') %}
         <link rel="author" title="{{ _('About these documents') }}"
@@ -85,29 +74,47 @@
   {%- endblock %}
   {%- block extrahead %} {% endblock %}
 
-  <script src="//cdnjs.cloudflare.com/ajax/libs/modernizr/2.6.2/modernizr.min.js"></script>
+  {# Keep modernizr in head - http://modernizr.com/docs/#installing #}
+  <script src="_static/js/modernizr.min.js"></script>
 
 </head>
 
-<body class="wy-body-for-nav">
+<body class="wy-body-for-nav" role="document">
 
   <div class="wy-grid-for-nav">
 
     {# SIDE NAV, TOGGLES ON MOBILE #}
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-nav-search">
-        <a href="{{ pathto(master_doc) }}" class="icon icon-home"> {{ project }}</a>
+        {% block sidebartitle %}
+
+        {% if logo and theme_logo_only %}
+          <a href="{{ pathto(master_doc) }}">
+        {% else %}
+          <a href="{{ pathto(master_doc) }}" class="icon icon-home"> {{ project }}
+        {% endif %}
+
+        {% if logo %}
+          {# Not strictly valid HTML, but it's the only way to display/scale it properly, without weird scripting or heaps of work #}
+          <img src="{{ pathto('_static/' + logo, 1) }}" class="logo" />
+        {% endif %}
+        </a>
+
         {% include "searchbox.html" %}
+
+        {% endblock %}
       </div>
 
-      <div class="wy-menu wy-menu-vertical" data-spy="affix">
-        {% set toctree = toctree(maxdepth=2, collapse=False, includehidden=True) %}
-        {% if toctree %}
-            {{ toctree }}
-        {% else %}
-            <!-- Local TOC -->
-            <div class="local-toc">{{ toc }}</div>
-        {% endif %}
+      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+        {% block menu %}
+          {% set toctree = toctree(maxdepth=4, collapse=False, includehidden=True) %}
+          {% if toctree %}
+              {{ toctree }}
+          {% else %}
+              <!-- Local TOC -->
+              <div class="local-toc">{{ toc }}</div>
+          {% endif %}
+        {% endblock %}
       </div>
       &nbsp;
     </nav>
@@ -115,8 +122,8 @@
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
 
       {# MOBILE NAV, TRIGGLES SIDE NAV ON TOGGLE #}
-      <nav class="wy-nav-top">
-        <i data-toggle="wy-nav-top" class="icon icon-reorder"></i>
+      <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
+        <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
         <a href="{{ pathto(master_doc) }}">{{ project }}</a>
       </nav>
 
@@ -125,7 +132,9 @@
       <div class="wy-nav-content">
         <div class="rst-content">
           {% include "breadcrumbs.html" %}
-          {% block body %}{% endblock %}
+          <div role="main" class="document">
+            {% block body %}{% endblock %}
+          </div>
           {% include "footer.html" %}
         </div>
       </div>
@@ -134,5 +143,39 @@
 
   </div>
   {% include "versions.html" %}
+
+  {% if not embedded %}
+
+    <script type="text/javascript">
+        var DOCUMENTATION_OPTIONS = {
+            URL_ROOT:'{{ url_root }}',
+            VERSION:'{{ release|e }}',
+            COLLAPSE_INDEX:false,
+            FILE_SUFFIX:'{{ '' if no_search_suffix else file_suffix }}',
+            HAS_SOURCE:  {{ has_source|lower }}
+        };
+    </script>
+    {%- for scriptfile in script_files %}
+      <script type="text/javascript" src="{{ pathto(scriptfile, 1) }}"></script>
+    {%- endfor %}
+
+  {% endif %}
+
+  {# RTD hosts this file, so just load on non RTD builds #}
+  {% if not READTHEDOCS %}
+    <script type="text/javascript" src="{{ pathto('_static/js/theme.js', 1) }}"></script>
+  {% endif %}
+
+  {# STICKY NAVIGATION #}
+  {% if theme_sticky_navigation %}
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.StickyNav.enable();
+      });
+  </script>
+  {% endif %}
+
+  {%- block footer %} {% endblock %}
+
 </body>
 </html>

lib/spack/docs/_themes/sphinx_rtd_theme/search.html

@@ -10,7 +10,7 @@
 {%- extends "layout.html" %}
 {% set title = _('Search') %}
 {% set script_files = script_files + ['_static/searchtools.js'] %}
-{% block extrahead %}
+{% block footer %}
   <script type="text/javascript">
     jQuery(function() { Search.loadIndex("{{ pathto('searchindex.js', 1) }}"); });
   </script>

lib/spack/docs/_themes/sphinx_rtd_theme/searchbox.html

@@ -1,5 +1,9 @@
-<form id ="rtd-search-form" class="wy-form" action="{{ pathto('search') }}" method="get">
-  <input type="text" name="q" placeholder="Search docs" />
-  <input type="hidden" name="check_keywords" value="yes" />
-  <input type="hidden" name="area" value="default" />
-</form>
+{%- if builder != 'singlehtml' %}
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="{{ pathto('search') }}" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+{%- endif %}

lib/spack/docs/_themes/sphinx_rtd_theme/static/css/badge_only.css

@@ -1 +1,2 @@
-.font-smooth,.icon:before{-webkit-font-smoothing:antialiased}.clearfix{*zoom:1}.clearfix:before,.clearfix:after{display:table;content:""}.clearfix:after{clear:both}@font-face{font-family:fontawesome-webfont;font-weight:normal;font-style:normal;src:url("../font/fontawesome_webfont.eot");src:url("../font/fontawesome_webfont.eot?#iefix") format("embedded-opentype"),url("../font/fontawesome_webfont.woff") format("woff"),url("../font/fontawesome_webfont.ttf") format("truetype"),url("../font/fontawesome_webfont.svg#fontawesome-webfont") format("svg")}.icon:before{display:inline-block;font-family:fontawesome-webfont;font-style:normal;font-weight:normal;line-height:1;text-decoration:inherit}a .icon{display:inline-block;text-decoration:inherit}li .icon{display:inline-block}li .icon-large:before,li .icon-large:before{width:1.875em}ul.icons{list-style-type:none;margin-left:2em;text-indent:-0.8em}ul.icons li .icon{width:0.8em}ul.icons li .icon-large:before,ul.icons li .icon-large:before{vertical-align:baseline}.icon-book:before{content:"\f02d"}.icon-caret-down:before{content:"\f0d7"}.icon-caret-up:before{content:"\f0d8"}.icon-caret-left:before{content:"\f0d9"}.icon-caret-right:before{content:"\f0da"}.rst-versions{position:fixed;bottom:0;left:0;width:300px;color:#fcfcfc;background:#1f1d1d;border-top:solid 10px #343131;font-family:"Lato","proxima-nova","Helvetica Neue",Arial,sans-serif;z-index:400}.rst-versions a{color:#2980b9;text-decoration:none}.rst-versions .rst-badge-small{display:none}.rst-versions .rst-current-version{padding:12px;background-color:#272525;display:block;text-align:right;font-size:90%;cursor:pointer;color:#27ae60;*zoom:1}.rst-versions .rst-current-version:before,.rst-versions .rst-current-version:after{display:table;content:""}.rst-versions .rst-current-version:after{clear:both}.rst-versions .rst-current-version .icon{color:#fcfcfc}.rst-versions .rst-current-version .icon-book{float:left}.rst-versions .rst-current-version.rst-out-of-date{background-color:#e74c3c;color:#fff}.rst-versions.shift-up .rst-other-versions{display:block}.rst-versions .rst-other-versions{font-size:90%;padding:12px;color:gray;display:none}.rst-versions .rst-other-versions hr{display:block;height:1px;border:0;margin:20px 0;padding:0;border-top:solid 1px #413d3d}.rst-versions .rst-other-versions dd{display:inline-block;margin:0}.rst-versions .rst-other-versions dd a{display:inline-block;padding:6px;color:#fcfcfc}.rst-versions.rst-badge{width:auto;bottom:20px;right:20px;left:auto;border:none;max-width:300px}.rst-versions.rst-badge .icon-book{float:none}.rst-versions.rst-badge.shift-up .rst-current-version{text-align:right}.rst-versions.rst-badge.shift-up .rst-current-version .icon-book{float:left}.rst-versions.rst-badge .rst-current-version{width:auto;height:30px;line-height:30px;padding:0 6px;display:block;text-align:center}@media screen and (max-width: 768px){.rst-versions{width:85%;display:none}.rst-versions.shift{display:block}img{width:100%;height:auto}}
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lib/spack/docs/_themes/sphinx_rtd_theme/static/js/theme.js

@@ -1,16 +1,113 @@
-$( document ).ready(function() {
-  // Shift nav in mobile when clicking the menu.
-  $("[data-toggle='wy-nav-top']").click(function() {
-    $("[data-toggle='wy-nav-shift']").toggleClass("shift");
-    $("[data-toggle='rst-versions']").toggleClass("shift");
-  });
-  // Close menu when you click a link.
-  $(".wy-menu-vertical .current ul li a").click(function() {
-    $("[data-toggle='wy-nav-shift']").removeClass("shift");
-    $("[data-toggle='rst-versions']").toggleClass("shift");
-  });
-  $("[data-toggle='rst-current-version']").click(function() {
-    $("[data-toggle='rst-versions']").toggleClass("shift-up");
-  });
-  $("table.docutils:not(.field-list").wrap("<div class='wy-table-responsive'></div>");
+function toggleCurrent (elem) {
+    var parent_li = elem.closest('li');
+    parent_li.siblings('li.current').removeClass('current');
+    parent_li.siblings().find('li.current').removeClass('current');
+    parent_li.find('> ul li.current').removeClass('current');
+    parent_li.toggleClass('current');
+}
+
+$(document).ready(function() {
+    // Shift nav in mobile when clicking the menu.
+    $(document).on('click', "[data-toggle='wy-nav-top']", function() {
+        $("[data-toggle='wy-nav-shift']").toggleClass("shift");
+        $("[data-toggle='rst-versions']").toggleClass("shift");
+    });
+    // Nav menu link click operations
+    $(document).on('click', ".wy-menu-vertical .current ul li a", function() {
+        var target = $(this);
+        // Close menu when you click a link.
+        $("[data-toggle='wy-nav-shift']").removeClass("shift");
+        $("[data-toggle='rst-versions']").toggleClass("shift");
+        // Handle dynamic display of l3 and l4 nav lists
+        toggleCurrent(target);
+        if (typeof(window.SphinxRtdTheme) != 'undefined') {
+            window.SphinxRtdTheme.StickyNav.hashChange();
+        }
+    });
+    $(document).on('click', "[data-toggle='rst-current-version']", function() {
+        $("[data-toggle='rst-versions']").toggleClass("shift-up");
+    });
+    // Make tables responsive
+    $("table.docutils:not(.field-list)").wrap("<div class='wy-table-responsive'></div>");
+
+    // Add expand links to all parents of nested ul
+    $('.wy-menu-vertical ul').siblings('a').each(function () {
+        var link = $(this);
+            expand = $('<span class="toctree-expand"></span>');
+        expand.on('click', function (ev) {
+            toggleCurrent(link);
+            ev.stopPropagation();
+            return false;
+        });
+        link.prepend(expand);
+    });
 });
+
+// Sphinx theme state
+window.SphinxRtdTheme = (function (jquery) {
+    var stickyNav = (function () {
+        var navBar,
+            win,
+            winScroll = false,
+            linkScroll = false,
+            winPosition = 0,
+            enable = function () {
+                init();
+                reset();
+                win.on('hashchange', reset);
+
+                // Set scrolling
+                win.on('scroll', function () {
+                    if (!linkScroll) {
+                        winScroll = true;
+                    }
+                });
+                setInterval(function () {
+                    if (winScroll) {
+                        winScroll = false;
+                        var newWinPosition = win.scrollTop(),
+                            navPosition = navBar.scrollTop(),
+                            newNavPosition = navPosition + (newWinPosition - winPosition);
+                        navBar.scrollTop(newNavPosition);
+                        winPosition = newWinPosition;
+                    }
+                }, 25);
+            },
+            init = function () {
+                navBar = jquery('nav.wy-nav-side:first');
+                win = jquery(window);
+            },
+            reset = function () {
+                // Get anchor from URL and open up nested nav
+                var anchor = encodeURI(window.location.hash);
+                if (anchor) {
+                    try {
+                        var link = $('.wy-menu-vertical')
+                            .find('[href="' + anchor + '"]');
+                        $('.wy-menu-vertical li.toctree-l1 li.current')
+                            .removeClass('current');
+                        link.closest('li.toctree-l2').addClass('current');
+                        link.closest('li.toctree-l3').addClass('current');
+                        link.closest('li.toctree-l4').addClass('current');
+                    }
+                    catch (err) {
+                        console.log("Error expanding nav for anchor", err);
+                    }
+                }
+            },
+            hashChange = function () {
+                linkScroll = true;
+                win.one('hashchange', function () {
+                    linkScroll = false;
+                });
+            };
+        jquery(init);
+        return {
+            enable: enable,
+            hashChange: hashChange
+        };
+    }());
+    return {
+        StickyNav: stickyNav
+    };
+}($));

lib/spack/docs/_themes/sphinx_rtd_theme/theme.conf

@@ -5,3 +5,5 @@ stylesheet = css/theme.css
 [options]
 typekit_id = hiw1hhg
 analytics_id = 
+sticky_navigation = False
+logo_only =

lib/spack/docs/_themes/sphinx_rtd_theme/versions.html

@@ -1,10 +1,10 @@
 {% if READTHEDOCS %}
 {# Add rst-badge after rst-versions for small badge style. #}
-  <div class="rst-versions" data-toggle="rst-versions">
+  <div class="rst-versions" data-toggle="rst-versions" role="note" aria-label="versions">
     <span class="rst-current-version" data-toggle="rst-current-version">
-      <span class="icon icon-book"> Read the Docs</span>
-      v: {{ current_version }} 
-      <span class="icon icon-caret-down"></span>
+      <span class="fa fa-book"> Read the Docs</span>
+      v: {{ current_version }}
+      <span class="fa fa-caret-down"></span>
     </span>
     <div class="rst-other-versions">
       <dl>

lib/spack/docs/case_studies.rst

@@ -0,0 +1,167 @@
+Using Spack for CMake-based Development
+==========================================
+
+These are instructions on how to use Spack to aid in the development
+of a CMake-based project.  Spack is used to help find the dependencies
+for the project, configure it at development time, and then package it
+it in a way that others can install.  Using Spack for CMake-based
+development consists of three parts:
+
+1. Setting up the CMake build in your software
+2. Writing the Spack Package
+3. Using it from Spack.
+
+
+Setting Up the CMake Build
+---------------------------------------
+
+You should follow standard CMake conventions in setting up your
+software, your CMake build should NOT depend on or require Spack to
+build.  See here for an example:
+   https://github.com/citibeth/icebin
+
+Note that there's one exception here to the rule I mentioned above.
+In ``CMakeLists.txt``, I have the following line::
+
+    include_directories($ENV{CMAKE_TRANSITIVE_INCLUDE_PATH})
+
+
+This is a hook into Spack, and it ensures that all transitive
+dependencies are included in the include path.  It's not needed if
+everything is in one tree, but it is (sometimes) in the Spack world;
+when running without Spack, it has no effect.
+
+Note that this "feature" is controversial, could break with future
+versions of GNU ld, and probably not the best to use.  The best
+practice is that you make sure that anything you #include is listed as
+a dependency in your CMakeLists.txt.
+
+To be more specific: if you #inlcude something from package A and an
+installed HEADER FILE in A #includes something from package B, then
+you should also list B as a dependency in your CMake build.  If you
+depend on A but header files exported by A do NOT #include things from
+B, then you do NOT need to list B as a dependency --- even if linking
+to A links in libB.so as well.
+
+I also recommend that you set up your CMake build to use RPATHs
+correctly.  Not only is this a good idea and nice, but it also ensures
+that your package will build the same with or without ``spack
+install``.
+
+Writing the Spack Package
+---------------------------------------
+
+Now that you have a CMake build, you want to tell Spack how to
+configure it.  This is done by writing a Spack package for your
+software.  See here for example:
+   https://github.com/citibeth/spack/blob/efischer/develop/var/spack/repos/builtin/packages/icebin/package.py
+
+You need to subclass ``CMakePackage``, as is done in this example.
+This enables advanced features of Spack for helping you in configuring
+your software (keep reading...).  Instead of an ``install()`` method
+used when subclassing ``Package``, you write ``configure_args()``.
+See here for more info on how this works:
+   https://github.com/LLNL/spack/pull/543/files
+
+NOTE: if your software is not publicly available, you do not need to
+set the URL or version.  Or you can set up bogus URLs and
+versions... whatever causes Spack to not crash.
+
+
+Using it from Spack
+--------------------------------
+
+Now that you have a Spack package, you can get Spack to setup your
+CMake project for you.  Use the following to setup, configure and
+build your project::
+
+    cd myproject
+    spack spconfig myproject@local
+    mkdir build; cd build
+    ../spconfig.py ..
+    make
+    make install
+
+
+Everything here should look pretty familiar here from a CMake
+perspective, except that ``spack spconfig`` creates the file
+``spconfig.py``, which calls CMake with arguments appropriate for your
+Spack configuration.  Think of it as the equivalent to running a bunch
+of ``spack location -i`` commands.  You will run ``spconfig.py``
+instead of running CMake directly.
+
+If your project is publicly available (eg on GitHub), then you can
+ALSO use this setup to "just install" a release version without going
+through the manual configuration/build step.  Just do:
+
+1. Put tag(s) on the version(s) in your GitHub repo you want to be release versions.
+
+2. Set the ``url`` in your ``package.py`` to download a tarball for
+   the appropriate version.  (GitHub will give you a tarball for any
+   version in the repo, if you tickle it the right way).  For example::
+
+    https://github.com/citibeth/icebin/tarball/v0.1.0
+
+   Set up versions as appropriate in your ``package.py``.  (Manually
+   download the tarball and run ``md5sum`` to determine the
+   appropriate checksum for it).
+
+3. Now you should be able to say ``spack install myproject@version``
+   and things "just work."
+
+NOTE... in order to use the features outlined in this post, you
+currently need to use the following branch of Spack:
+   https://github.com/citibeth/spack/tree/efischer/develop
+
+There is a pull request open on this branch (
+https://github.com/LLNL/spack/pull/543 ) and we are working to get it
+integrated into the main ``develop`` branch.
+
+
+Activating your Software
+-------------------------------------
+
+Once you've built your software, you will want to load it up.  You can
+use ``spack load mypackage@local`` for that in your ``.bashrc``, but
+that is slow.  Try stuff like the following instead:
+
+The following command will load the Spack-installed packages needed
+for basic Python use of IceBin::
+
+    module load `spack module find tcl icebin netcdf cmake@3.5.1`
+    module load `spack module find --dependencies tcl py-basemap py-giss`
+
+
+You can speed up shell startup by turning these into ``module load`` commands.
+
+1. Cut-n-paste the script ``make_spackenv``::
+
+    #!/bin/sh
+    #
+    # Generate commands to load the Spack environment
+
+    SPACKENV=$HOME/spackenv.sh
+
+    spack module find --shell tcl git icebin@local ibmisc netcdf cmake@3.5.1 >$SPACKENV
+    spack module find --dependencies --shell tcl py-basemap py-giss >>$SPACKENV
+
+2. Add the following to your ``.bashrc`` file::
+
+    source $HOME/spackenv.sh
+    # Preferentially use your checked-out Python source
+    export PYTHONPATH=$HOME/icebin/pylib:$PYTHONPATH
+
+3. Run ``sh make_spackenv`` whenever your Spack installation changes (including right now).
+
+
+Giving Back
+-------------------
+
+If your software is publicly available, you should submit the
+``package.py`` for it as a pull request to the main Spack GitHub
+project.  This will ensure that anyone can install your software
+(almost) painlessly with a simple ``spack install`` command.  See here
+for how that has turned into detailed instructions that have
+successfully enabled collaborators to install complex software:
+
+   https://github.com/citibeth/icebin/blob/develop/README.rst

lib/spack/docs/conf.py

@@ -6,7 +6,7 @@
 # Written 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
@@ -43,6 +43,7 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.insert(0, os.path.abspath('exts'))
+sys.path.insert(0, os.path.abspath('../external'))
 
 # Add the Spack bin directory to the path so that we can use its output in docs.
 spack_root = '../../..'
@@ -50,7 +51,8 @@
 os.environ['PATH'] += os.pathsep + '$SPACK_ROOT/bin'
 
 spack_version =  subprocess.Popen(
-    ['spack', '-V'], stderr=subprocess.PIPE).communicate()[1].strip().split('.')
+    [spack_root + '/bin/spack', '-V'],
+    stderr=subprocess.PIPE).communicate()[1].strip().split('.')
 
 # Set an environment variable so that colify will print output like it would to
 # a terminal.
@@ -87,14 +89,14 @@
 source_suffix = '.rst'
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+source_encoding = 'utf-8-sig'
 
 # The master toctree document.
 master_doc = 'index'
 
 # General information about the project.
 project = u'Spack'
-copyright = u'2013-2014, Lawrence Livermore National Laboratory'
+copyright = u'2013-2015, Lawrence Livermore National Laboratory.'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -149,7 +151,7 @@
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = []
+html_theme_options = { 'logo_only' : True }
 
 # Add any paths that contain custom themes here, relative to this directory.
 html_theme_path = ["_themes"]
@@ -163,12 +165,12 @@
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+html_logo = '../../../share/spack/logo/spack-logo-white-text-48.png'
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = None
+html_favicon = '../../../share/spack/logo/favicon.ico'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -203,7 +205,7 @@
 #html_show_sourcelink = True
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
+#html_show_sphinx = False
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
 #html_show_copyright = True

lib/spack/docs/configuration.rst

@@ -0,0 +1,236 @@
+.. _configuration:
+
+Configuration
+===================================
+
+.. _temp-space:
+
+Temporary space
+----------------------------
+
+.. warning:: Temporary space configuration will eventually be moved to
+   configuration files, but currently these settings are in
+   ``lib/spack/spack/__init__.py``
+
+By default, Spack will try to do all of its building in temporary
+space.  There are two main reasons for this.  First, Spack is designed
+to run out of a user's home directory, and on may systems the home
+directory is network mounted and potentially not a very fast
+filesystem.  We create build stages in a temporary directory to avoid
+this.  Second, many systems impose quotas on home directories, and
+``/tmp`` or similar directories often have more available space.  This
+helps conserve space for installations in users' home directories.
+
+You can customize temporary directories by editing
+``lib/spack/spack/__init__.py``.  Specifically, find this part of the file:
+
+.. code-block:: python
+
+   # Whether to build in tmp space or directly in the stage_path.
+   # If this is true, then spack will make stage directories in
+   # a tmp filesystem, and it will symlink them into stage_path.
+   use_tmp_stage = True
+
+   # Locations to use for staging and building, in order of preference
+   # Use a %u to add a username to the stage paths here, in case this
+   # is a shared filesystem.  Spack will use the first of these paths
+   # that it can create.
+   tmp_dirs = ['/nfs/tmp2/%u/spack-stage',
+               '/var/tmp/%u/spack-stage',
+               '/tmp/%u/spack-stage']
+
+The ``use_tmp_stage`` variable controls whether Spack builds
+**directly** inside the ``var/spack/`` directory.  Normally, Spack
+will try to find a temporary directory for a build, then it *symlinks*
+that temporary directory into ``var/spack/`` so that you can keep
+track of what temporary directories Spack is using.
+
+The ``tmp_dirs`` variable is a list of paths Spack should search when
+trying to find a temporary directory.  They can optionally contain a
+``%u``, which will substitute the current user's name into the path.
+The list is searched in order, and Spack will create a temporary stage
+in the first directory it finds to which it has write access.  Add
+more elements to the list to indicate where your own site's temporary
+directory is.
+
+.. _sec-external_packages:
+
+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
+that should be used instead of Spack building its own MPI.
+
+External packages are configured through the ``packages.yaml`` file found
+in a Spack installation's ``etc/spack/`` or a user's ``~/.spack/``
+directory. Here's an example of an external configuration:
+
+.. code-block:: yaml
+
+   packages:
+      openmpi:
+         paths:
+            openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7: /opt/openmpi-1.4.3
+            openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7+debug: /opt/openmpi-1.4.3-debug
+            openmpi@1.6.5%intel@10.1 arch=linux-x86_64-debian7: /opt/openmpi-1.6.5-intel
+
+This example lists three installations of OpenMPI, one built with gcc,
+one built with gcc and debug information, and another built with Intel.
+If Spack is asked to build a package that uses one of these MPIs as a
+dependency, it will use the the pre-installed OpenMPI in
+the given directory. Packages.yaml can also be used to specify modules
+
+Each ``packages.yaml`` begins with a ``packages:`` token, followed
+by a list of package names.  To specify externals, add a ``paths`` or ``modules``
+token under the package name, which lists externals in a
+``spec: /path`` or ``spec: module-name`` format.  Each spec should be as
+well-defined as reasonably possible.  If a
+package lacks a spec component, such as missing a compiler or
+package version, then Spack will guess the missing component based
+on its most-favored packages, and it may guess incorrectly.
+
+Each package version and compilers listed in an external should
+have entries in Spack's packages and compiler configuration, even
+though the package and compiler may not every be built.
+
+The packages configuration can tell Spack to use an external location
+for certain package versions, but it does not restrict Spack to using
+external packages.  In the above example, if an OpenMPI 1.8.4 became
+available Spack may choose to start building and linking with that version
+rather than continue using the pre-installed OpenMPI versions.
+
+To prevent this, the ``packages.yaml`` configuration also allows packages
+to be flagged as non-buildable.  The previous example could be modified to
+be:
+
+.. code-block:: yaml
+
+  packages:
+    openmpi:
+      paths:
+        openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7: /opt/openmpi-1.4.3
+        openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7+debug: /opt/openmpi-1.4.3-debug
+        openmpi@1.6.5%intel@10.1 arch=linux-x86_64-debian7: /opt/openmpi-1.6.5-intel
+      buildable: False
+
+The addition of the ``buildable`` flag tells Spack that it should never build
+its own version of OpenMPI, and it will instead always rely on a pre-built
+OpenMPI.  Similar to ``paths``, ``buildable`` is specified as a property under
+a package name.
+
+If an external module is specified as not buildable, then Spack will load the
+external module into the build environment which can be used for linking.
+
+The ``buildable`` does not need to be paired with external packages.
+It could also be used alone to forbid packages that may be
+buggy or otherwise undesirable.
+
+
+Concretization Preferences
+--------------------------------
+
+Spack can be configured to prefer certain compilers, package
+versions, depends_on, and variants during concretization.
+The preferred configuration can be controlled via the
+``~/.spack/packages.yaml`` file for user configuations, or the
+``etc/spack/packages.yaml`` site configuration.
+
+
+Here's an example packages.yaml file that sets preferred packages:
+
+.. code-block:: sh
+
+    packages:
+      opencv:
+        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 opencv 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 opencv, 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,
+supply ``-p`` to Spack on the command line, before any subcommands.
+
+.. _spack-p:
+
+``spack -p``
+~~~~~~~~~~~~~~~~~
+
+``spack -p`` output looks like this:
+
+.. code-block:: sh
+
+   $ spack -p graph dyninst
+   o  dyninst
+   |\
+   | |\
+   | o |  libdwarf
+   |/ /
+   o |  libelf
+    /
+   o  boost
+
+         307670 function calls (305943 primitive calls) in 0.127 seconds
+
+   Ordered by: internal time
+
+   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
+      853    0.021    0.000    0.066    0.000 inspect.py:472(getmodule)
+    51197    0.011    0.000    0.018    0.000 inspect.py:51(ismodule)
+    73961    0.010    0.000    0.010    0.000 {isinstance}
+     1762    0.006    0.000    0.053    0.000 inspect.py:440(getsourcefile)
+    32075    0.006    0.000    0.006    0.000 {hasattr}
+     1760    0.004    0.000    0.004    0.000 {posix.stat}
+     2240    0.004    0.000    0.004    0.000 {posix.lstat}
+     2602    0.004    0.000    0.011    0.000 inspect.py:398(getfile)
+      771    0.004    0.000    0.077    0.000 inspect.py:518(findsource)
+     2656    0.004    0.000    0.004    0.000 {method 'match' of '_sre.SRE_Pattern' objects}
+    30772    0.003    0.000    0.003    0.000 {method 'get' of 'dict' objects}
+    ...
+
+The bottom of the output shows the top most time consuming functions,
+slowest on top.  The profiling support is from Python's built-in tool,
+`cProfile
+<https://docs.python.org/2/library/profile.html#module-cProfile>`_.

lib/spack/docs/developer_guide.rst

@@ -73,19 +73,33 @@ with a high level view of Spack's directory structure::
   spack/                  <- installation root
      bin/
         spack             <- main spack executable
+
+     etc/
+        spack/            <- Spack config files.
+                             Can be overridden by files in ~/.spack.
+
      var/
         spack/            <- build & stage directories
+            repos/            <- contains package repositories
+               builtin/       <- pkg repository that comes with Spack
+                  repo.yaml   <- descriptor for the builtin repository
+                  packages/   <- directories under here contain packages
+            cache/        <- saves resources downloaded during installs
+
      opt/
         spack/            <- packages are installed here
+
      lib/
         spack/
            docs/          <- source for this documentation
            env/           <- compiler wrappers for build environment
 
+           external/      <- external libs included in Spack distro
+           llnl/          <- some general-use libraries
+
            spack/         <- spack module; contains Python code
               cmd/        <- each file in here is a spack subcommand
               compilers/  <- compiler description files
-              packages/   <- each file in here is a spack package
               test/       <- unit test modules
               util/       <- common code
 

lib/spack/docs/exts/sphinxcontrib/__init__.py

@@ -6,7 +6,7 @@
 # Written 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

lib/spack/docs/exts/sphinxcontrib/programoutput.py

@@ -6,7 +6,7 @@
 # Written 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

lib/spack/docs/features.rst

@@ -31,14 +31,21 @@ platform, all on the command line.
    # Specify a compiler (and its version), with %
    $ spack install mpileaks@1.1.2 %gcc@4.7.3
 
-   # Add special compile-time options with +
+   # Add special compile-time options by name
+   $ spack install mpileaks@1.1.2 %gcc@4.7.3 debug=True
+
+   # Add special boolean compile-time options with +
    $ spack install mpileaks@1.1.2 %gcc@4.7.3 +debug
 
-   # Cross-compile for a different architecture with =
-   $ spack install mpileaks@1.1.2 =bgqos_0
+   # Add compiler flags using the conventional names
+   $ spack install mpileaks@1.1.2 %gcc@4.7.3 cppflags=\"-O3 -floop-block\"
 
-Users can specify as many or few options as they care about.  Spack
-will fill in the unspecified values with sensible defaults.
+   # Cross-compile for a different architecture with arch=
+   $ spack install mpileaks@1.1.2 arch=bgqos_0
+
+Users can specify as many or few options as they care about. Spack
+will fill in the unspecified values with sensible defaults. The two listed
+syntaxes for variants are identical when the value is boolean.
 
 
 Customize dependencies
@@ -103,7 +110,7 @@ creates a simple python file:
 It doesn't take much python coding to get from there to a working
 package:
 
-.. literalinclude:: ../../../var/spack/packages/libelf/package.py
+.. literalinclude:: ../../../var/spack/repos/builtin/packages/libelf/package.py
    :lines: 25-
 
 Spack also provides wrapper functions around common commands like

lib/spack/docs/getting_started.rst

@@ -1,35 +1,98 @@
 Getting Started
 ====================
 
-Download
+Prerequisites
+---------------
+
+Spack has the following minimum requirements, which must be installed
+before Spack is run:
+
+1. Operating System: GNU/Linux or Macintosh
+2. Python 2.6 or 2.7
+3. A C/C++ compiler
+
+These requirements can be easily installed on most modern Linux
+systems; on Macintosh, XCode is required.
+
+
+Installation
 --------------------
 
 Getting spack is easy.  You can clone it from the `github repository
-<https://github.com/scalability-llnl/spack>`_ using this command:
+<https://github.com/llnl/spack>`_ using this command:
 
 .. code-block:: sh
 
-   $ git clone https://github.com/scalability-llnl/spack.git
+   $ git clone https://github.com/llnl/spack.git
 
-This will create a directory called ``spack``.  We'll assume that the
-full path to this directory is in some environment called
-``SPACK_HOME``.  Add ``$SPACK_HOME/bin`` to your path and you're ready
-to go:
+This will create a directory called ``spack``.  If you are using Spack
+for a specific purpose, you might have received different instructions
+on how to download Spack; if so, please follow those instructions.
+
+Add Spack to Shell
+~~~~~~~~~~~~~~~~~~~
+
+We'll assume that the full path to your downloaded Spack directory is
+in the ``SPACK_ROOT`` environment variable.  Add ``$SPACK_ROOT/bin``
+to your path and you're ready to go:
 
 .. code-block:: sh
 
-   $ export PATH=spack/bin:$PATH
+   $ export PATH=$SPACK_ROOT/bin:$PATH
    $ spack install libelf
 
-In general, most of your interactions with Spack will be through the
-``spack`` command.
+For a richer experience, use Spack's `shell support
+<http://software.llnl.gov/spack/basic_usage.html#environment-modules>`_:
+
+.. code-block:: sh
+
+   # For bash users
+   $ . $SPACK_ROOT/share/spack/setup-env.sh
+
+   # For tcsh or csh users (note you must set SPACK_ROOT)
+   $ setenv SPACK_ROOT /path/to/spack
+   $ source $SPACK_ROOT/share/spack/setup-env.csh
+
+This automatically adds Spack to your ``PATH``.
+
+Clean Environment
+~~~~~~~~~~~~~~~~~~
+
+Many packages' installs can be broken by changing environment
+variables.  For example, a packge might pick up the wrong build-time
+dependencies (most of them not specified) depending on the setting of
+``PATH``.  ``GCC`` seems to be particularly vulnerable to these issues.
+
+Therefore, it is recommended that Spack users run with a *clean
+environment*, especially for ``PATH``.  Only software that comes with
+the system, or that you know you wish to use with Spack, should be
+included.  This procedure will avoid many strange build errors that no
+one knows how to fix.
 
 
-Install
---------------------
+Although Spack will work as soon as you clone it, it won't necessarily
+be able to install any packages.  That is because Spack relies 
 
-You don't need to install Spack; it's ready to run as soon as you
-clone it from git.
+Check Installation
+~~~~~~~~~~~~~~~~~~~~~
+
+With Spack installed, you should be able to run some basic Spack commands.  For example:
+
+.. code-block:: sh
+
+    $ spack spec netcdf
+      ...
+      netcdf@4.4.1%gcc@5.3.0~hdf4+mpi arch=linux-SuSE11-x86_64
+          ^curl@7.50.1%gcc@5.3.0 arch=linux-SuSE11-x86_64
+              ^openssl@system%gcc@5.3.0 arch=linux-SuSE11-x86_64
+              ^zlib@1.2.8%gcc@5.3.0 arch=linux-SuSE11-x86_64
+          ^hdf5@1.10.0-patch1%gcc@5.3.0+cxx~debug+fortran+mpi+shared~szip~threadsafe arch=linux-SuSE11-x86_64
+              ^openmpi@1.10.1%gcc@5.3.0~mxm~pmi~psm~psm2~slurm~sqlite3~thread_multiple~tm+verbs+vt arch=linux-SuSE11-x86_64
+          ^m4@1.4.17%gcc@5.3.0+sigsegv arch=linux-SuSE11-x86_64
+              ^libsigsegv@2.10%gcc@5.3.0 arch=linux-SuSE11-x86_64
+
+Optional: Alternate Prefix
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 You may want to run it out of a prefix other than the git repository
 you cloned.  The ``spack bootstrap`` command provides this
@@ -39,6 +102,675 @@ functionality.  To install spack in a new directory, simply type:
 
     $ spack bootstrap /my/favorite/prefix
 
-This will install a new spack script in /my/favorite/prefix/bin, which
-you can use just like you would the regular spack script.  Each copy
-of spack installs packages into its own ``$PREFIX/opt`` directory.
+This will install a new spack script in ``/my/favorite/prefix/bin``,
+which you can use just like you would the regular spack script.  Each
+copy of spack installs packages into its own ``$PREFIX/opt``
+directory.
+
+
+
+
+.. _compiler-config:
+
+Compiler configuration
+-----------------------------------
+
+Spack has the ability to build packages with multiple compilers and
+compiler versions. Spack searches for compilers on your machine
+automatically the first time it is run. It does this by inspecting
+your path.
+
+.. _spack-compilers:
+
+``spack compilers``
+~~~~~~~~~~~~~~~~~~~~~~~
+
+You can see which compilers spack has found by running ``spack
+compilers`` or ``spack compiler list``::
+
+    $ spack compilers
+    ==> Available compilers
+    -- gcc ---------------------------------------------------------
+        gcc@4.9.0  gcc@4.8.0  gcc@4.7.0  gcc@4.6.2  gcc@4.4.7
+        gcc@4.8.2  gcc@4.7.1  gcc@4.6.3  gcc@4.6.1  gcc@4.1.2
+    -- intel -------------------------------------------------------
+        intel@15.0.0  intel@14.0.0  intel@13.0.0  intel@12.1.0  intel@10.0
+        intel@14.0.3  intel@13.1.1  intel@12.1.5  intel@12.0.4  intel@9.1
+        intel@14.0.2  intel@13.1.0  intel@12.1.3  intel@11.1
+        intel@14.0.1  intel@13.0.1  intel@12.1.2  intel@10.1
+    -- clang -------------------------------------------------------
+        clang@3.4  clang@3.3  clang@3.2  clang@3.1
+    -- pgi ---------------------------------------------------------
+        pgi@14.3-0   pgi@13.2-0  pgi@12.1-0   pgi@10.9-0  pgi@8.0-1
+        pgi@13.10-0  pgi@13.1-1  pgi@11.10-0  pgi@10.2-0  pgi@7.1-3
+        pgi@13.6-0   pgi@12.8-0  pgi@11.1-0   pgi@9.0-4   pgi@7.0-6
+
+Any of these compilers can be used to build Spack packages.  More on
+how this is done is in :ref:`sec-specs`.
+
+.. _spack-compiler-add:
+
+``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 find`` with the path to
+where the compiler is installed.  For example::
+
+    $ 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 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 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 add it to
+``PATH``, and then it adds the compiler to Spack.
+
+.. _spack-compiler-info:
+
+``spack compiler info``
+~~~~~~~~~~~~~~~~~~~~~~~
+
+If you want to see specifics on a particular compiler, you can run
+``spack compiler info`` on it::
+
+   $ spack compiler info intel@15
+   intel@15.0.0:
+           cc  = /usr/local/bin/icc-15.0.090
+           cxx = /usr/local/bin/icpc-15.0.090
+           f77 = /usr/local/bin/ifort-15.0.090
+           fc  = /usr/local/bin/ifort-15.0.090
+
+This shows which C, C++, and Fortran compilers were detected by Spack.
+Notice also that we didn\'t have to be too specific about the
+version. We just said ``intel@15``, and information about the only
+matching Intel compiler was displayed.
+
+
+Manual Compiler Configuration
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If auto-detection fails, you can manually configure a compiler by
+editing your ``~/.spack/compilers.yaml`` file.  You can do this by running
+``spack config edit compilers``, which will open the file in your ``$EDITOR``.
+
+Each compiler configuration in the file looks like this::
+
+    ...
+    compilers:
+      - compiler:
+          modules = []
+          operating_system: OS
+        paths:
+          cc: /usr/local/bin/icc-15.0.024-beta
+          cxx: /usr/local/bin/icpc-15.0.024-beta
+          f77: /usr/local/bin/ifort-15.0.024-beta
+          fc: /usr/local/bin/ifort-15.0.024-beta
+
+          spec: intel@15.0.0:
+
+For compilers, like ``clang``, that do not support Fortran, put
+``None`` for ``f77`` and ``fc``::
+
+    clang@3.3svn:
+        cc: /usr/bin/clang
+        cxx: /usr/bin/clang++
+        f77: None
+        fc: None
+
+Once you save the file, the configured compilers will show up in the
+list displayed by ``spack compilers``.
+
+You can also add compiler flags to manually configured compilers. The
+valid flags are ``cflags``, ``cxxflags``, ``fflags``, ``cppflags``,
+``ldflags``, and ``ldlibs``. For example::
+
+    ...
+    compilers:
+      - compiler:
+      ...
+      intel@15.0.0:
+          cc: /usr/local/bin/icc-15.0.024-beta
+          cxx: /usr/local/bin/icpc-15.0.024-beta
+          f77: /usr/local/bin/ifort-15.0.024-beta
+          fc: /usr/local/bin/ifort-15.0.024-beta
+          cppflags: -O3 -fPIC
+      ...
+
+These flags will be treated by spack as if they were enterred from
+the command line each time this compiler is used. The compiler wrappers
+then inject those flags into the compiler command. Compiler flags
+enterred from the command line will be discussed in more detail in the
+following section.
+
+
+Build Your Own Compiler
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If you are particular about which compiler/version you use, you might
+wish to have Spack build it for you.  For example:
+
+.. code-block::
+
+    spack install gcc@4.9.3
+
+Once that has finished, you will need to add it to your
+``compilers.yaml`` file.  If this is your preferred compiler, in
+general future Spack builds will use it.
+
+.. note::
+
+    If you are building your own compiler, it can be useful to have a
+    Spack instance just for that.  For example, create a new Spack in
+    ``~/spack-tools`` and then run ``~/spack-tools/bin/spack install
+    gcc@4.9.3``.  Once the compiler is built, don't build anything
+    more in that Spack instance; instead, create a new "real" Spack
+    instance, configure Spack to use the compiler you've just built,
+    and then build your application software in the new Spack
+    instance.
+
+    This tip is useful because sometimes you will find yourself
+    rebuilding may pacakges due to Spack updates.  Sometimes, you
+    might even delete your entire Spack installation and start fresh.
+    If your compiler was built in a separate Spack installation, you
+    will never have to rebuild it --- as long as you wish to continue
+    using that version of the compiler.
+
+
+Compilers Requiring Modules
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Many installed compilers will work regardless of the environment they
+are called with.  However, some installed compilers require
+``$LD_LIBRARY_PATH`` or other environment variables to be set in order
+to run; Intel compilers are known for this.  In such a case, you
+should tell Spack which module(s) to load in order to run the chosen
+compiler.  Spack will load this module into the environment ONLY when
+the compiler is run, and NOT in general for a package's ``install()``
+method.  See, for example, this ``compilers.yaml`` file:
+
+.. code-block:: yaml
+
+    compilers:
+    - compiler:
+        modules: [other/comp/gcc-5.3-sp3]
+        operating_system: SuSE11
+        paths:
+          cc: /usr/local/other/SLES11.3/gcc/5.3.0/bin/gcc
+          cxx: /usr/local/other/SLES11.3/gcc/5.3.0/bin/g++
+          f77: /usr/local/other/SLES11.3/gcc/5.3.0/bin/gfortran
+          fc: /usr/local/other/SLES11.3/gcc/5.3.0/bin/gfortran
+        spec: gcc@5.3.0
+
+Some compilers require a module to be loaded not just to run, but also
+to execute any code built with the compiler, breaking packages that
+execute any bits of code they just compiled.  Such compilers should be
+taken behind the barn and put out of their misery.  If that is not
+possible or practical, the user (and anyone running code built by that
+compiler) will need to load the compiler's module into their
+environment.  And ``spack install --dirty`` will need to be used.
+
+Compiler Verification
+~~~~~~~~~~~~~~~~~~~~~~
+
+You can verify that your compilers are configured properly by installing a
+simple package.  For example:
+
+.. code-block:: sh
+
+    spack install zlib%gcc@5.3.0
+
+
+System Packages
+-----------------
+
+Once compilers are configured, one needs to determine which
+pre-installed system packages, if any, to use in builds.  This is
+configured in the file `~/.spack/packages.yaml`.  For example, to use
+an OpenMPI installed in /opt/local, one would use:
+
+.. code-block:: yaml
+
+    packages:
+        openmpi:
+            paths:
+                openmpi@1.10.1: /opt/local
+            buildable: False
+
+In general, Spack is easier to use and more reliable if it builds all
+its own dependencies.  However, there are two packages for which one
+commonly needs to use system versions:
+
+MPI
+~~~
+
+On supercomputers, sysadmins have already built MPI versions that take
+into account the specifics of that computer's hardware.  Unless you
+know how they were built and can choose the correct Spack variants,
+you are unlikely to get a working MPI from Spack.  Instead, use an
+appropraite pre-installed MPI.
+
+If you choose a pre-installed MPI, you should consider using the
+pre-installed compiler used to build that MPI; see above on
+``compilers.yaml``.
+
+OpenSSL
+~~~~~~~~
+
+The ``openssl`` package underlies much of modern security in a modern
+OS; an attacker can easily "pwn" any computer on which can modify SSL.
+Therefore, any `openssl` used on a system should be created in a
+"trusted environment" --- for example, that of the OS vendor.
+
+OpenSSL is also updated by the OS vendor from time to time, in
+response to security problems discovered in the wider community.  It
+is in everyone's best interest to use any newly updated versions as
+soon as they come out.  Modern Linux installations have standard
+procedures for security updates without user involvement.
+
+Spack running at user-level is not a trusted environment, nor do Spack
+users generally keep up-to-date on the latest security holes in SSL.
+For these reasons, any Spack-installed OpenSSL should be considered
+untrusted.
+
+As long as the system-provided SSL works, it is better to use it.  One can check if it works by trying to download an ``https://``.  For example:
+
+.. code-block:: sh
+
+    curl -O https://github.com/ImageMagick/ImageMagick/archive/7.0.2-7.tar.gz
+
+As long as it works, the recommended way to tell Spack to use the
+system-supplied OpenSSL is to add the following to ``packages.yaml``.
+Note that the ``@system`` "version" means "I don't care what version
+it is, just use what is there."  This is appropraite for OpenSSL,
+which has a stable API.
+
+
+.. code-block:: yaml
+
+    packages:
+        # Recommended for security reasons
+        # Do not install OpenSSL as non-root user.
+        openssl:
+            paths:
+                openssl@system: /usr
+            version: [system]
+            buildable: False
+
+
+
+Utilities Configuration
+-------------------------
+
+Although Spack does not need installation *per se*, it does rely on
+other packages to be available on its host system.  If those packages
+are out of date or missing, then Spack will not work.  Sometimes, an
+appeal to the system's package manager can fix such problems.  If not,
+the solution is have Spack install the required packages, and then
+have Spack use them.
+
+For example, if `curl` doesn't work, one could use the following steps
+to provide Spack a working `curl`:
+
+.. code-block:: sh
+
+    $ spack install curl
+    $ spack load curl
+
+or alternately:
+
+.. code-block:: sh
+
+    $ spack module loads curl >>~/.bashrc
+
+or if environment modules don't work:
+
+.. code-block:: sh
+
+    $ export PATH=`spack location -i curl`/bin:$PATH
+
+
+External commands are used by Spack in two places: within core Spack,
+and in the package recipes. The bootstrapping procedure for these two
+cases is somewhat different, and is treated separately below.
+
+Core Spack Utilities
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Core Spack uses the following packages, aminly to download and unpack
+source code, and to load generated environment modules: ``curl``,
+``env``, ``git``, ``go``, ``hg``, ``svn``, ``tar``, ``unzip``,
+``patch``, ``environment-modules``.
+
+As long as the user's environment is set up to successfully run these
+programs from outside of Spack, they should work inside of Spack as
+well.  They can generally be activated as in the `curl` example above;
+or some systems might already have an appropriate hand-built
+environment module that may be loaded.  Either way works.
+
+A few notes on specific programs in this list:
+
+cURL, git, Mercurial, etc.
+```````````````````````````
+
+Spack depends on cURL to download tarballs, the format that most
+Spack-installed packages come in.  Your system's cURL should always be
+able to download unencrypted ``http://``.  However, the cURL on some
+systems has problems with SSL-enabled ``https://`` URLs, due to
+outdated / insecure versions of OpenSSL on those systems.  This will
+prevent Spack from installing any software requiring ``https://``
+until a new cURL has been installed, using the technique above.
+
+.. note::
+
+    ``curl`` depends on ``openssl`` and ``zlib``, both of which are
+    downloadable from non-SSL sources.  Unfortunately, this
+    Spack-built cURL should be considered untrustworthy for
+    ``https://`` sources becuase it relies on an OpenSSL built in user
+    space.  Luckily, Spack verifies checksums of the software it
+    installs, and does not rely on a secure SSL implementation.
+
+    If your version of ``curl`` is not trustworthy, then you should
+    not use it outside of Spack.  Instead of putting it in your
+    ``.bashrc``, you might wish to create a short shell script that
+    loads the appropariate module(s) and then launches Spack.
+
+Some packages use source code control systems as their download
+method: ``git``, ``hg``, ``svn`` and occasionally ``go``.  If you had
+to install a new ``curl``, then chances are the system-supplied
+version of these other programs will also not work, because they also
+rely on OpenSSL.  Once ``curl`` has been installed, the others should
+also be installable.
+
+
+.. _InstallEnvironmentModules:
+
+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.
+For example: ```yum install environment-modules``
+(Fedora/RHEL/CentOS).  If your Linux distribution does not have
+Environment Modules, you can get it with Spack:
+
+1. Consider using system tcl (as long as your system has Tcl version 8.0 or later):
+    1. Identify its location using ``which tclsh``
+    2. Identify its version using ``echo 'puts $tcl_version;exit 0' | tclsh``
+    3. Add to ``~/.spack/packages.yaml`` and modify as appropriate:
+
+       .. code-block:: yaml
+
+           packages:
+               tcl:
+                   paths:
+                       tcl@8.5: /usr
+                   version: [8.5]
+                   buildable: False
+
+2. Install with::
+   .. code-block:: sh
+
+       spack install environment-modules
+
+3. Activate with the following script (or apply the updates to your
+   ``.bashrc`` file manually)::
+
+   .. code-block:: sh
+
+       TMP=`tempfile`
+       echo >$TMP
+       MODULE_HOME=`spack location -i environment-modules`
+       MODULE_VERSION=`ls -1 $MODULE_HOME/Modules | head -1`
+       ${MODULE_HOME}/Modules/${MODULE_VERSION}/bin/add.modules <$TMP
+       cp .bashrc $TMP
+       echo "MODULE_VERSION=${MODULE_VERSION}" > .bashrc
+       cat $TMP >>.bashrc
+
+This adds to your ``.bashrc`` (or similar) files, enabling Environment
+Modules when you log in.  Re-load your .bashrc (or log out and in
+again), and then test that the ``module`` command is found with:
+
+.. code-block:: sh
+
+    module avail
+
+
+Package Utilities
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Spack can also encounter bootstrapping problems inside a package's
+``install()`` method.  In this case, Spack will normally be running
+inside a *sanitized build environment*.  This includes all of the
+package's dependencies, but none of the environment Spack inherited
+from the user: if you load a module or modify ``$PATH`` before
+launching Spack, it will have no effect.
+
+In this case, you will likley need to use the ``--dirty`` flag when
+running ``spack install``, causing Spack to **not** santize the build
+environment.  You are now responsible for making sure that environment
+does not do strange things to Spack or its installs.
+
+Another way to get Spack to use its own version of something is to add that something to a package that needs it.  For example:
+
+.. code-block:: python
+
+    depends_on('binutils', type='build')
+
+This is considered best practice for some common build dependencies,
+such as ``autotools`` (if the ``autoreconf`` command is needed) and
+``cmake`` --- ``cmake`` especially, because different packages require
+a different version of CMake.
+
+However, adding ``depends_on('binutils')`` to every package is not
+considered a best practice because every package written in
+C/C++/Fortran would need it.  Loading a recent ``binutils`` into your
+environment is preferable here.
+
+binutils
+~~~~~~~~~
+
+# https://groups.google.com/forum/#!topic/spack/i_7l_kEEveI
+
+Sometimes, strange error messages can happen while building a package.
+For exmaple, ``ld`` might crash.  Or one receives a message like:
+
+.. code-block::
+
+    ld: final link failed: Nonrepresentable section on output
+
+These problems are often caused by an outdated ``binutils`` on your
+system: bootstrap as described above.
+
+Install 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.
+For example: ```yum install environment-modules``
+(Fedora/RHEL/CentOS).  If your Linux distribution does not have
+Environment Modules, you can get it with Spack:
+
+1. Consider using system tcl.  If so, add to ``packages.yaml``::
+
+    packages:
+        tcl:
+            paths:
+                tcl@8.5: /usr
+            version: [8.5]
+            buildable: False
+2. Install with::
+
+    spack install environment-modules
+
+3. Activate with::
+
+    TMP=`tempfile`
+    echo >$TMP
+    MODULE_HOME=`spack location -i environment-modules`
+    MODULE_VERSION=`ls -1 $MODULE_HOME/Modules | head -1`
+    ${MODULE_HOME}/Modules/${MODULE_VERSION}/bin/add.modules <$TMP
+    cp .bashrc $TMP
+    echo "MODULE_VERSION=${MODULE_VERSION}" > .bashrc
+    cat $TMP >>.bashrc
+
+This adds to your ``.bashrc`` (or similar) files, enabling Environment
+Modules when you log in.  Re-load your .bashrc (or log out and in
+again), and then test that the ``module`` command is found with:
+
+    module avail
+
+
+Spack on Cray
+-----------------------------
+
+Spack differs slightly when used on a Cray system. The architecture spec
+can differentiate between the front-end and back-end processor and operating system.
+For example, on Edison at NERSC, the back-end target processor
+is \"Ivy Bridge\", so you can specify to use the back-end this way:
+
+.. code-block:: sh
+
+    spack install zlib target=ivybridge
+
+You can also use the operating system to build against the back-end:
+
+.. code-block:: sh
+
+    spack install zlib os=CNL10
+
+Notice that the name includes both the operating system name and the major
+version number concatenated together.
+
+Alternatively, if you want to build something for the front-end,
+you can specify the front-end target processor. The processor for a login node
+on Edison is \"Sandy bridge\" so we specify on the command line like so:
+
+.. code-block:: sh
+
+    spack install zlib target=sandybridge
+
+And the front-end operating system is:
+
+.. code-block:: sh
+
+    spack install zlib os=SuSE11
+
+
+
+Cray compiler detection
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Spack can detect compilers using two methods. For the front-end, we treat
+everything the same. The difference lies in back-end compiler detection.
+Back-end compiler detection is made via the Tcl module avail command.
+Once it detects the compiler it writes the appropriate PrgEnv and compiler
+module name to compilers.yaml and sets the paths to each compiler with Cray\'s
+compiler wrapper names (i.e. cc, CC, ftn). During build time, Spack will load
+the correct PrgEnv and compiler module and will call appropriate wrapper.
+
+The compilers.yaml config file will also differ. There is a
+modules section that is filled with the compiler\'s Programming Environment
+and module name. On other systems, this field is empty []::
+
+    ...
+    - compiler:
+        modules:
+          - PrgEnv-intel
+          - intel/15.0.109
+    ...
+
+As mentioned earlier, the compiler paths will look different on a Cray system.
+Since most compilers are invoked using cc, CC and ftn, the paths for each
+compiler are replaced with their respective Cray compiler wrapper names::
+
+    ...
+     paths:
+       cc: cc
+       cxx: CC
+       f77: ftn
+       fc: ftn
+    ...
+
+As opposed to an explicit path to the compiler executable. This allows Spack
+to call the Cray compiler wrappers during build time.
+
+For more on compiler configuration, check out :ref:`compiler-config`.
+
+Spack sets the default Cray link type to dynamic, to better match other
+other platforms. Individual packages can enable static linking (which is the
+default outside of Spack on cray systems) using the -static flag.
+
+Setting defaults and using Cray modules
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If you want to use default compilers for each PrgEnv and also be able
+to load cray external modules, you will need to set up a packages.yaml.
+
+Here\'s an example of an external configuration for cray modules:
+
+.. code-block:: yaml
+
+  packages:
+      mpi:
+        modules:
+            mpich@7.3.1%gcc@5.2.0 arch=cray_xc-haswell-CNL10: cray-mpich
+            mpich@7.3.1%intel@16.0.0.109 arch=cray_xc-haswell-CNL10: cray-mpich
+
+This tells Spack that for whatever package that depends on mpi, load the
+cray-mpich module into the environment. You can then be able to use whatever
+environment variables, libraries, etc, that are brought into the environment
+via module load.
+
+You can set the default compiler that Spack can use for each compiler type.
+If you want to use the Cray defaults, then set them under *all:* in packages.yaml.
+In the compiler field, set the compiler specs in your order of preference.
+Whenever you build with that compiler type, Spack will concretize to that version.
+
+Here is an example of a full packages.yaml used at NERSC
+
+.. code-block:: yaml
+
+   packages:
+    mpi:
+        modules:
+            mpich@7.3.1%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge: cray-mpich
+            mpich@7.3.1%intel@16.0.0.109 arch=cray_xc-SuSE11-ivybridge: cray-mpich
+        buildable: False
+    netcdf:
+        modules:
+            netcdf@4.3.3.1%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge: cray-netcdf
+            netcdf@4.3.3.1%intel@16.0.0.109 arch=cray_xc-CNL10-ivybridge: cray-netcdf
+        buildable: False
+    hdf5:
+        modules:
+            hdf5@1.8.14%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge: cray-hdf5
+            hdf5@1.8.14%intel@16.0.0.109 arch=cray_xc-CNL10-ivybridge: cray-hdf5
+        buildable: False
+    all:
+        compiler: [gcc@5.2.0, intel@16.0.0.109]
+
+Here we tell spack that whenever we want to build with gcc use version 5.2.0 or
+if we want to build with intel compilers, use version 16.0.0.109. We add a spec
+for each compiler type for each cray modules. This ensures that for each
+compiler on our system we can use that external module.
+
+
+For more on external packages check out the section :ref:`sec-external_packages`.

lib/spack/docs/index.rst

@@ -18,18 +18,18 @@ configurations can coexist on the same system.
 Most importantly, Spack is *simple*.  It offers a simple *spec* syntax
 so that users can specify versions and configuration options
 concisely.  Spack is also simple for package authors: package files
-are writtin in pure Python, and specs allow package authors to write a
-single build script for many different builds of the same package.
+are written in pure Python, and specs allow package authors to
+maintain a single file for many different builds of the same package.
 
 See the :doc:`features` for examples and highlights.
 
 Get spack from the `github repository
-<https://github.com/scalability-llnl/spack>`_ and install your first
+<https://github.com/llnl/spack>`_ and install your first
 package:
 
 .. code-block:: sh
 
-   $ git clone https://github.com/scalability-llnl/spack.git
+   $ git clone https://github.com/llnl/spack.git
    $ cd spack/bin
    $ ./spack install libelf
 
@@ -46,9 +46,11 @@ Table of Contents
    getting_started
    basic_usage
    packaging_guide
+   application_developer_support
    mirrors
-   site_configuration
+   configuration
    developer_guide
+   case_studies
    command_index
    package_list
    API Docs <spack>

lib/spack/docs/mirrors.rst

@@ -38,7 +38,7 @@ contains tarballs for each package, named after each package.
 
 .. note::
 
-   Archives are **not** named exactly they were in the package's fetch
+   Archives are **not** named exactly the way they were in the package's fetch
    URL.  They have the form ``<name>-<version>.<extension>``, where
    ``<name>`` is Spack's name for the package, ``<version>`` is the
    version of the tarball, and ``<extension>`` is whatever format the
@@ -186,7 +186,7 @@ Each mirror has a name so that you can refer to it again later.
 ``spack mirror list``
 ----------------------------
 
-If you want to see all the mirrors Spack knows about you can run ``spack mirror list``::
+To see all the mirrors Spack knows about, run ``spack mirror list``::
 
    $ spack mirror list
    local_filesystem    file:///Users/gamblin2/spack-mirror-2014-06-24
@@ -196,7 +196,7 @@ If you want to see all the mirrors Spack knows about you can run ``spack mirror
 ``spack mirror remove``
 ----------------------------
 
-And, if you want to remove a mirror, just remove it by name::
+To remove a mirror by name::
 
    $ spack mirror remove local_filesystem
    $ spack mirror list
@@ -205,13 +205,30 @@ And, if you want to remove a mirror, just remove it by name::
 Mirror precedence
 ----------------------------
 
-Adding a mirror really just adds a section in ``~/.spackconfig``::
+Adding a mirror really adds a line in ``~/.spack/mirrors.yaml``::
 
-   [mirror "local_filesystem"]
-       url = file:///Users/gamblin2/spack-mirror-2014-06-24
-   [mirror "remote_server"]
-       url = https://example.com/some/web-hosted/directory/spack-mirror-2014-06-24
+   mirrors:
+     local_filesystem: file:///Users/gamblin2/spack-mirror-2014-06-24
+     remote_server: https://example.com/some/web-hosted/directory/spack-mirror-2014-06-24
 
 If you want to change the order in which mirrors are searched for
 packages, you can edit this file and reorder the sections.  Spack will
 search the topmost mirror first and the bottom-most mirror last.
+
+.. _caching:
+
+Local Default Cache
+----------------------------
+
+Spack caches resources that are downloaded as part of installs. The cache is
+a valid spack mirror: it uses the same directory structure and naming scheme
+as other Spack mirrors (so it can be copied anywhere and referenced with a URL
+like other mirrors). The mirror is maintained locally (within the Spack 
+installation directory) at :file:`var/spack/cache/`. It is always enabled (and 
+is always searched first when attempting to retrieve files for an installation) 
+but can be cleared with :ref:`purge <spack-purge>`; the cache directory can also
+be deleted manually without issue. 
+
+Caching includes retrieved tarball archives and source control repositories, but
+only resources with an associated digest or commit ID (e.g. a revision number 
+for SVN) will be cached.

lib/spack/docs/packaging_guide.rst

@@ -36,10 +36,11 @@ Creating & editing packages
 ``spack create``
 ~~~~~~~~~~~~~~~~~~~~~
 
-The ``spack create`` command generates a boilerplate package template
-from a URL.  The URL should point to a tarball or other software
-archive.  In most cases, ``spack create`` plus a few modifications is
-all you need to get a package working.
+The ``spack create`` command creates a directory with the package name and
+generates a ``package.py`` file with a boilerplate package template from a URL.
+The URL should point to a tarball or other software archive.  In most cases,
+``spack create`` plus a few modifications is all you need to get a package
+working.
 
 Here's an example:
 
@@ -47,12 +48,16 @@ Here's an example:
 
    $ spack create http://www.cmake.org/files/v2.8/cmake-2.8.12.1.tar.gz
 
-Spack examines the tarball URL and tries to figure out the name of the
-package to be created. It also tries to determine what version strings
-look like for this package. Using this information, it will try to
-find *additional* versions by spidering the package's webpage.  If it
-finds multiple versions, Spack prompts you to tell it how many
-versions you want to download and checksum:
+Spack examines the tarball URL and tries to figure out the name of the package
+to be created. Once the name is determined a directory in the appropriate
+repository is created with that name. Spack prefers, but does not require, that
+names be lower case so the directory name will be lower case when ``spack
+create`` generates it. In cases where it is desired to have mixed case or upper
+case simply rename the directory. Spack also tries to determine what version
+strings look like for this package. Using this information, it will try to find
+*additional* versions by spidering the package's webpage.  If it finds multiple
+versions, Spack prompts you to tell it how many versions you want to download
+and checksum:
 
 .. code-block:: sh
 
@@ -84,7 +89,7 @@ always choose to download just one tarball initially, and run
 
    If it fails entirely, you can get minimal boilerplate by using
    :ref:`spack-edit-f`, or you can manually create a directory and
-   ``package.py`` file for the package in ``var/spack/packages``.
+   ``package.py`` file for the package in ``var/spack/repos/builtin/packages``.
 
 .. note::
 
@@ -203,7 +208,7 @@ edit`` command:
 So, if you used ``spack create`` to create a package, then saved and
 closed the resulting file, you can get back to it with ``spack edit``.
 The ``cmake`` package actually lives in
-``$SPACK_ROOT/var/spack/packages/cmake/package.py``, but this provides
+``$SPACK_ROOT/var/spack/repos/builtin/packages/cmake/package.py``, but this provides
 a much simpler shortcut and saves you the trouble of typing the full
 path.
 
@@ -269,18 +274,18 @@ live in Spack's directory structure.  In general, `spack-create`_ and
 `spack-edit`_ handle creating package files for you, so you can skip
 most of the details here.
 
-``var/spack/packages``
+``var/spack/repos/builtin/packages``
 ~~~~~~~~~~~~~~~~~~~~~~~
 
 A Spack installation directory is structured like a standard UNIX
 install prefix (``bin``, ``lib``, ``include``, ``var``, ``opt``,
 etc.).  Most of the code for Spack lives in ``$SPACK_ROOT/lib/spack``.
-Packages themselves live in ``$SPACK_ROOT/var/spack/packages``.
+Packages themselves live in ``$SPACK_ROOT/var/spack/repos/builtin/packages``.
 
 If you ``cd`` to that directory, you will see directories for each
 package:
 
-.. command-output::  cd $SPACK_ROOT/var/spack/packages;  ls -CF
+.. command-output::  cd $SPACK_ROOT/var/spack/repos/builtin/packages;  ls -CF
    :shell:
    :ellipsis: 10
 
@@ -288,7 +293,7 @@ Each directory contains a file called ``package.py``, which is where
 all the python code for the package goes.  For example, the ``libelf``
 package lives in::
 
-   $SPACK_ROOT/var/spack/packages/libelf/package.py
+   $SPACK_ROOT/var/spack/repos/builtin/packages/libelf/package.py
 
 Alongside the ``package.py`` file, a package may contain extra
 directories or files (like patches) that it needs to build.
@@ -297,11 +302,12 @@ directories or files (like patches) that it needs to build.
 Package Names
 ~~~~~~~~~~~~~~~~~~
 
-Packages are named after the directory containing ``package.py``.  So,
-``libelf``'s ``package.py`` lives in a directory called ``libelf``.
-The ``package.py`` file defines a class called ``Libelf``, which
+Packages are named after the directory containing ``package.py``. It is
+preferred, but not required, that the directory, and thus the package name, are
+lower case. So, ``libelf``'s ``package.py`` lives in a directory called
+``libelf``.  The ``package.py`` file defines a class called ``Libelf``, which
 extends Spack's ``Package`` class.  for example, here is
-``$SPACK_ROOT/var/spack/packages/libelf/package.py``:
+``$SPACK_ROOT/var/spack/repos/builtin/packages/libelf/package.py``:
 
 .. code-block:: python
    :linenos:
@@ -328,7 +334,7 @@ these:
    $ spack install libelf@0.8.13
 
 Spack sees the package name in the spec and looks for
-``libelf/package.py`` in ``var/spack/packages``.  Likewise, if you say
+``libelf/package.py`` in ``var/spack/repos/builtin/packages``.  Likewise, if you say
 ``spack install py-numpy``, then Spack looks for
 ``py-numpy/package.py``.
 
@@ -377,6 +383,8 @@ add a line like this in the package class:
        version('8.2.1', '4136d7b4c04df68b686570afa26988ac')
        ...
 
+Versions should be listed with the newest version first.
+
 Version URLs
 ~~~~~~~~~~~~~~~~~
 
@@ -385,8 +393,22 @@ in the package.  For example, Spack is smart enough to download
 version ``8.2.1.`` of the ``Foo`` package above from
 ``http://example.com/foo-8.2.1.tar.gz``.
 
-If spack *cannot* extrapolate the URL from the ``url`` field, or if
-the package doesn't have a ``url`` field, you can add a URL explicitly
+If spack *cannot* extrapolate the URL from the ``url`` field by
+default, you can write your own URL generation algorithm in place of
+the ``url`` declaration.  For example:
+
+.. code-block:: python
+   :linenos:
+
+   class Foo(Package):
+       version('8.2.1', '4136d7b4c04df68b686570afa26988ac')
+       ...
+       def url_for_version(self, version):
+           return 'http://example.com/version_%s/foo-%s.tar.gz' \
+               % (version, version)
+       ...
+
+If a URL cannot be derived systematically, you can add an explicit URL
 for a particular version:
 
 .. code-block:: python
@@ -401,6 +423,35 @@ construct the new one for ``8.2.1``.
 When you supply a custom URL for a version, Spack uses that URL
 *verbatim* and does not perform extrapolation.
 
+Skipping the expand step
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Spack normally expands archives automatically after downloading
+them. If you want to skip this step (e.g., for self-extracting
+executables and other custom archive types), you can add
+``expand=False`` to a ``version`` directive.
+
+.. code-block:: python
+
+   version('8.2.1', '4136d7b4c04df68b686570afa26988ac',
+           url='http://example.com/foo-8.2.1-special-version.tar.gz', expand=False)
+
+When ``expand`` is set to ``False``, Spack sets the current working
+directory to the directory containing the downloaded archive before it
+calls your ``install`` method.  Within ``install``, the path to the
+downloaded archive is available as ``self.stage.archive_file``.
+
+Here is an example snippet for packages distributed as self-extracting
+archives.  The example sets permissions on the downloaded file to make
+it executable, then runs it with some arguments.
+
+.. code-block:: python
+
+   def install(self, spec, prefix):
+       set_executable(self.stage.archive_file)
+       installer = Executable(self.stage.archive_file)
+       installer('--prefix=%s' % prefix, 'arg1', 'arg2', 'etc.')
+
 Checksums
 ~~~~~~~~~~~~~~~~~
 
@@ -417,14 +468,25 @@ to use based on the hash length.
 ``spack md5``
 ^^^^^^^^^^^^^^^^^^^^^^
 
-If you have a single file to checksum, you can use the ``spack md5``
-command to do it.  Here's how you might download an archive and get a
-checksum for it:
+If you have one or more files to checksum, you can use the ``spack md5``
+command to do it:
 
 .. code-block:: sh
 
-   $ curl -O http://exmaple.com/foo-8.2.1.tar.gz'
-   $ spack md5 foo-8.2.1.tar.gz
+   $ spack md5 foo-8.2.1.tar.gz foo-8.2.2.tar.gz
+   ==> 2 MD5 checksums:
+   4136d7b4c04df68b686570afa26988ac  foo-8.2.1.tar.gz
+   1586b70a49dfe05da5fcc29ef239dce0  foo-8.2.2.tar.gz
+
+``spack md5`` also accepts one or more URLs and automatically downloads
+the files for you:
+
+.. code-block:: sh
+
+   $ spack md5 http://example.com/foo-8.2.1.tar.gz
+   ==> Trying to fetch from http://example.com/foo-8.2.1.tar.gz
+   ######################################################################## 100.0%
+   ==> 1 MD5 checksum:
    4136d7b4c04df68b686570afa26988ac  foo-8.2.1.tar.gz
 
 Doing this for lots of files, or whenever a new package version is
@@ -518,7 +580,7 @@ The package author is responsible for coming up with a sensible name
 for each version to be fetched from a repository.  For example, if
 you're fetching from a tag like ``v1.0``, you might call that ``1.0``.
 If you're fetching a nameless git commit or an older subversion
-revision, you might give the commit an intuitive name, like ``dev``
+revision, you might give the commit an intuitive name, like ``develop``
 for a development version, or ``some-fancy-new-feature`` if you want
 to be more specific.
 
@@ -528,6 +590,17 @@ branches move forward over time and you aren't guaranteed to get the
 same thing every time you fetch a particular version.  Life isn't
 always simple, though, so this is not strictly enforced.
 
+When fetching from from the branch corresponding to the development version
+(often called ``master``,``trunk`` or ``dev``), it is recommended to
+call this version ``develop``. Spack has special treatment for this version so
+ that ``@develop`` will satisfy dependencies like
+``depends_on(abc, when="@x.y.z:")``. In other words, ``@develop`` is
+greater than any other version. The rationale is that certain features or
+options first appear in the development branch. Therefore if a package author
+wants to keep the package on the bleeding edge and provide support for new
+features, it is advised to use ``develop`` for such a version which will
+greatly simplify writing dependencies and version-related conditionals.
+
 In some future release, Spack may support extrapolating repository
 versions as it does for tarball URLs, but currently this is not
 supported.
@@ -543,6 +616,7 @@ Git fetching is enabled with the following parameters to ``version``:
   * ``tag``: name of a tag to fetch.
   * ``branch``: name of a branch to fetch.
   * ``commit``: SHA hash (or prefix) of a commit to fetch.
+  * ``submodules``: Also fetch submodules when checking out this repository.
 
 Only one of ``tag``, ``branch``, or ``commit`` can be used at a time.
 
@@ -553,7 +627,7 @@ Default branch
 
      class Example(Package):
          ...
-         version('dev', git='https://github.com/example-project/example.git')
+         version('develop', git='https://github.com/example-project/example.git')
 
   This is not recommended, as the contents of the default branch
   change over time.
@@ -599,6 +673,17 @@ Commits
   could just use the abbreviated commit hash.  It's up to the package
   author to decide what makes the most sense.
 
+Submodules
+
+  You can supply ``submodules=True`` to cause Spack to fetch submodules
+  along with the repository at fetch time.
+
+  .. code-block:: python
+
+     version('1.0.1', git='https://github.com/example-project/example.git',
+             tag='v1.0.1', submdoules=True)
+
+
 Installing
 ^^^^^^^^^^^^^^
 
@@ -626,13 +711,13 @@ Default
 
   .. code-block:: python
 
-     version('hg-head', hg='https://jay.grs.rwth-aachen.de/hg/example')
+     version('develop', hg='https://jay.grs.rwth-aachen.de/hg/example')
 
   Note that this is not recommended; try to fetch a particular
   revision instead.
 
 Revisions
-  Add ``hg`` and ``revision``parameters:
+  Add ``hg`` and ``revision`` parameters:
 
   .. code-block:: python
 
@@ -658,7 +743,7 @@ Fetching the head
 
   .. code-block:: python
 
-     version('svn-head', svn='https://outreach.scidac.gov/svn/libmonitor/trunk')
+     version('develop', svn='https://outreach.scidac.gov/svn/libmonitor/trunk')
 
   This is not recommended, as the head will move forward over time.
 
@@ -668,12 +753,140 @@ Fetching a revision
 
   .. code-block:: python
 
-     version('svn-head', svn='https://outreach.scidac.gov/svn/libmonitor/trunk',
+     version('develop', svn='https://outreach.scidac.gov/svn/libmonitor/trunk',
              revision=128)
 
 Subversion branches are handled as part of the directory structure, so
 you can check out a branch or tag by changing the ``url``.
 
+Automatic caching of files fetched during installation
+------------------------------------------------------
+
+Spack maintains a cache (described :ref:`here <caching>`) which saves files
+retrieved during package installations to avoid re-downloading in the case that
+a package is installed with a different specification (but the same version) or
+reinstalled on account of a change in the hashing scheme.
+
+.. _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:: sh
+
+    # 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:: sh
+
+    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
@@ -703,7 +916,7 @@ supply is a filename, then the patch needs to live within the spack
 source tree.  For example, the patch above lives in a directory
 structure like this::
 
-   $SPACK_ROOT/var/spack/packages/
+   $SPACK_ROOT/var/spack/repos/builtin/packages/
        mvapich2/
            package.py
            ad_lustre_rwcontig_open_source.patch
@@ -1071,11 +1284,13 @@ just as easily provide a version range:
 
    depends_on("libelf@0.8.2:0.8.4:")
 
-Or a requirement for a particular variant:
+Or a requirement for a particular variant or compiler flags:
 
 .. code-block:: python
 
    depends_on("libelf@0.8+debug")
+   depends_on('libelf debug=True')
+   depends_on('libelf cppflags="-fPIC")
 
 Both users *and* package authors can use the same spec syntax to refer
 to different package configurations.  Users use the spec syntax on the
@@ -1083,6 +1298,31 @@ command line to find installed packages or to install packages with
 particular constraints, and package authors can use specs to describe
 relationships between packages.
 
+Additionally, dependencies may be specified for specific use cases:
+
+.. code-block:: python
+
+    depends_on("cmake", type="build")
+    depends_on("libelf", type=("build", "link"))
+    depends_on("python", type="run")
+
+The dependency types are:
+
+  * **"build"**: made available during the project's build. The package will
+    be added to ``PATH``, the compiler include paths, and ``PYTHONPATH``.
+    Other projects which depend on this one will not have these modified
+    (building project X doesn't need project Y's build dependencies).
+  * **"link"**: the project is linked to by the project. The package will be
+    added to the current package's ``rpath``.
+  * **"run"**: the project is used by the project at runtime. The package will
+    be added to ``PATH`` and ``PYTHONPATH``.
+
+If not specified, ``type`` is assumed to be ``("build", "link")``. This is the
+common case for compiled language usage. Also available are the aliases
+``"alldeps"`` for all dependency types and ``"nolink"`` (``("build", "run")``)
+for use by dependencies which are not expressed via a linker (e.g., Python or
+Lua module loading).
+
 .. _setup-dependent-environment:
 
 ``setup_dependent_environment()``
@@ -1187,6 +1427,19 @@ Now, the ``py-numpy`` package can be used as an argument to ``spack
 activate``.  When it is activated, all the files in its prefix will be
 symbolically linked into the prefix of the python package.
 
+Many packages produce Python extensions for *some* variants, but not
+others: they should extend ``python`` only if the apropriate
+variant(s) are selected.  This may be accomplished with conditional
+``extends()`` declarations:
+
+.. code-block:: python
+
+   class FooLib(Package):
+       variant('python', default=True, description= \
+           'Build the Python extension Module')
+       extends('python', when='+python')
+       ...
+
 Sometimes, certain files in one package will conflict with those in
 another, which means they cannot both be activated (symlinked) at the
 same time.  In this case, you can tell Spack to ignore those files
@@ -1473,21 +1726,21 @@ the user runs ``spack install`` and the time the ``install()`` method
 is called.  The concretized version of the spec above might look like
 this::
 
-   mpileaks@2.3%gcc@4.7.3=linux-ppc64
-       ^callpath@1.0%gcc@4.7.3+debug=linux-ppc64
-           ^dyninst@8.1.2%gcc@4.7.3=linux-ppc64
-               ^libdwarf@20130729%gcc@4.7.3=linux-ppc64
-                   ^libelf@0.8.11%gcc@4.7.3=linux-ppc64
-           ^mpich@3.0.4%gcc@4.7.3=linux-ppc64
+   mpileaks@2.3%gcc@4.7.3 arch=linux-debian7-x86_64
+       ^callpath@1.0%gcc@4.7.3+debug arch=linux-debian7-x86_64
+           ^dyninst@8.1.2%gcc@4.7.3 arch=linux-debian7-x86_64
+               ^libdwarf@20130729%gcc@4.7.3 arch=linux-debian7-x86_64
+                   ^libelf@0.8.11%gcc@4.7.3 arch=linux-debian7-x86_64
+           ^mpich@3.0.4%gcc@4.7.3 arch=linux-debian7-x86_64
 
 .. graphviz::
 
    digraph {
-       "mpileaks@2.3\n%gcc@4.7.3\n=linux-ppc64" -> "mpich@3.0.4\n%gcc@4.7.3\n=linux-ppc64"
-       "mpileaks@2.3\n%gcc@4.7.3\n=linux-ppc64" -> "callpath@1.0\n%gcc@4.7.3+debug\n=linux-ppc64" -> "mpich@3.0.4\n%gcc@4.7.3\n=linux-ppc64"
-       "callpath@1.0\n%gcc@4.7.3+debug\n=linux-ppc64" -> "dyninst@8.1.2\n%gcc@4.7.3\n=linux-ppc64"
-       "dyninst@8.1.2\n%gcc@4.7.3\n=linux-ppc64" -> "libdwarf@20130729\n%gcc@4.7.3\n=linux-ppc64" -> "libelf@0.8.11\n%gcc@4.7.3\n=linux-ppc64"
-       "dyninst@8.1.2\n%gcc@4.7.3\n=linux-ppc64" -> "libelf@0.8.11\n%gcc@4.7.3\n=linux-ppc64"
+       "mpileaks@2.3\n%gcc@4.7.3\n arch=linux-debian7-x86_64" -> "mpich@3.0.4\n%gcc@4.7.3\n arch=linux-debian7-x86_64"
+       "mpileaks@2.3\n%gcc@4.7.3\n arch=linux-debian7-x86_64" -> "callpath@1.0\n%gcc@4.7.3+debug\n arch=linux-debian7-x86_64" -> "mpich@3.0.4\n%gcc@4.7.3\n arch=linux-debian7-x86_64"
+       "callpath@1.0\n%gcc@4.7.3+debug\n arch=linux-debian7-x86_64" -> "dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-debian7-x86_64"
+       "dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-debian7-x86_64" -> "libdwarf@20130729\n%gcc@4.7.3\n arch=linux-debian7-x86_64" -> "libelf@0.8.11\n%gcc@4.7.3\n arch=linux-debian7-x86_64"
+       "dyninst@8.1.2\n%gcc@4.7.3\n arch=linux-debian7-x86_64" -> "libelf@0.8.11\n%gcc@4.7.3\n arch=linux-debian7-x86_64"
    }
 
 Here, all versions, compilers, and platforms are filled in, and there
@@ -1498,8 +1751,8 @@ point will Spack call the ``install()`` method for your package.
 Concretization in Spack is based on certain selection policies that
 tell Spack how to select, e.g., a version, when one is not specified
 explicitly.  Concretization policies are discussed in more detail in
-:ref:`site-configuration`.  Sites using Spack can customize them to
-match the preferences of their own users.
+:ref:`configuration`.  Sites using Spack can customize them to match
+the preferences of their own users.
 
 .. _spack-spec:
 
@@ -1516,14 +1769,25 @@ running ``spack spec``.  For example:
        ^libdwarf
            ^libelf
 
-   dyninst@8.0.1%gcc@4.7.3=linux-ppc64
-       ^libdwarf@20130729%gcc@4.7.3=linux-ppc64
-           ^libelf@0.8.13%gcc@4.7.3=linux-ppc64
+   dyninst@8.0.1%gcc@4.7.3 arch=linux-debian7-x86_64
+       ^libdwarf@20130729%gcc@4.7.3 arch=linux-debian7-x86_64
+           ^libelf@0.8.13%gcc@4.7.3 arch=linux-debian7-x86_64
 
 This is useful when you want to know exactly what Spack will do when
 you ask for a particular spec.
 
 
+``Concretization Policies``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+A user may have certain preferences for how packages should
+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.
+
+See the `documentation in the config section <concretization-preferences_>`_
+for more details.
+
 .. _install-method:
 
 Implementing the ``install`` method
@@ -1533,7 +1797,7 @@ The last element of a package is its ``install()`` method.  This is
 where the real work of installation happens, and it's the main part of
 the package you'll need to customize for each piece of software.
 
-.. literalinclude::  ../../../var/spack/packages/libelf/package.py
+.. literalinclude::  ../../../var/spack/repos/builtin/packages/libelf/package.py
    :start-after: 0.8.12
    :linenos:
 
@@ -1681,7 +1945,7 @@ discover its dependencies.
 
 If you want to see the environment that a package will build with, or
 if you want to run commands in that environment to test them out, you
-can use the :ref:```spack env`` <spack-env>` command, documented
+can use the :ref:`spack env <spack-env>` command, documented
 below.
 
 .. _compiler-wrappers:
@@ -1711,15 +1975,15 @@ Compile-time library search paths
   * ``-L$dep_prefix/lib``
   * ``-L$dep_prefix/lib64``
 Runtime library search paths (RPATHs)
-  * ``-Wl,-rpath=$dep_prefix/lib``
-  * ``-Wl,-rpath=$dep_prefix/lib64``
+  * ``$rpath_flag$dep_prefix/lib``
+  * ``$rpath_flag$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
@@ -1739,6 +2003,67 @@ 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``.
+
+The compiler wrappers also pass the compiler flags specified by the user from
+the command line (``cflags``, ``cxxflags``, ``fflags``, ``cppflags``, ``ldflags``,
+and/or ``ldlibs``). They do not override the canonical autotools flags with the
+same names (but in ALL-CAPS) that may be passed into the build by particularly
+challenging package scripts.
+
+Compiler flags
+~~~~~~~~~~~~~~
+In rare circumstances such as compiling and running small unit tests, a package
+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.
+
+
+Blas and Lapack libraries
+~~~~~~~~~~~~~~~~~~~~~~~~~
+Different packages provide implementation of ``Blas`` and ``Lapack`` routines.
+The names of the resulting static and/or shared libraries differ from package
+to package. In order to make ``install()`` method indifferent to the
+choice of ``Blas`` implementation, each package which provides it
+sets up ``self.spec.blas_shared_lib`` and ``self.spec.blas_static_lib `` to
+point to the shared and static ``Blas`` libraries, respectively. The same
+applies to packages which provide ``Lapack``. Package developers are advised to
+use these variables, for example ``spec['blas'].blas_shared_lib`` instead of
+hard-coding ``join_path(spec['blas'].prefix.lib, 'libopenblas.so')``.
+
+
 Forking ``install()``
 ~~~~~~~~~~~~~~~~~~~~~
 
@@ -1752,6 +2077,20 @@ dedicated process.
 
 .. _prefix-objects:
 
+
+Failing the build
+----------------------
+
+Sometimes you don't want a package to successfully install unless some
+condition is true.  You can explicitly cause the build to fail from
+``install()`` by raising an ``InstallError``, for example:
+
+.. code-block:: python
+
+   if spec.architecture.startswith('darwin'):
+       raise InstallError('This package does not build on Mac OS X!')
+
+
 Prefix objects
 ----------------------
 
@@ -1937,12 +2276,12 @@ example:
        def install(self, prefix):
            # Do default install
 
-       @when('=chaos_5_x86_64_ib')
+       @when('arch=linux-debian7-x86_64')
        def install(self, prefix):
            # This will be executed instead of the default install if
            # the package's sys_type() is chaos_5_x86_64_ib.
 
-       @when('=bgqos_0")
+       @when('arch=linux-debian7-x86_64")
        def install(self, prefix):
            # This will be executed if the package's sys_type is bgqos_0
 
@@ -2068,6 +2407,62 @@ package, this allows us to avoid race conditions in the library's
 build system.
 
 
+.. _sanity-checks:
+
+Sanity checking an installation
+--------------------------------
+
+By default, Spack assumes that a build has failed if nothing is
+written to the install prefix, and that it has succeeded if anything
+(a file, a directory, etc.)  is written to the install prefix after
+``install()`` completes.
+
+Consider a simple autotools build like this:
+
+.. code-block:: python
+
+   def install(self, spec, prefix):
+       configure("--prefix=" + prefix)
+       make()
+       make("install")
+
+If you are using using standard autotools or CMake, ``configure`` and
+``make`` will not write anything to the install prefix.  Only ``make
+install`` writes the files, and only once the build is already
+complete.  Not all builds are like this.  Many builds of scientific
+software modify the install prefix *before* ``make install``. Builds
+like this can falsely report that they were successfully installed if
+an error occurs before the install is complete but after files have
+been written to the ``prefix``.
+
+
+``sanity_check_is_file`` and ``sanity_check_is_dir``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+You can optionally specify *sanity checks* to deal with this problem.
+Add properties like this to your package:
+
+.. code-block:: python
+
+   class MyPackage(Package):
+       ...
+
+       sanity_check_is_file = ['include/libelf.h']
+       sanity_check_is_dir  = [lib]
+
+       def install(self, spec, prefix):
+           configure("--prefix=" + prefix)
+           make()
+           make("install")
+
+Now, after ``install()`` runs, Spack will check whether
+``$prefix/include/libelf.h`` exists and is a file, and whether
+``$prefix/lib`` exists and is a directory.  If the checks fail, then
+the build will fail and the install prefix will be removed.  If they
+succeed, Spack considers the build succeeful and keeps the prefix in
+place.
+
+
 .. _file-manipulation:
 
 File manipulation functions
@@ -2108,6 +2503,15 @@ Filtering functions
 
   Examples:
 
+  #. Filtering a Makefile to force it to use Spack's compiler wrappers:
+
+     .. code-block:: python
+
+        filter_file(r'^CC\s*=.*',  spack_cc,  'Makefile')
+        filter_file(r'^CXX\s*=.*', spack_cxx, 'Makefile')
+        filter_file(r'^F77\s*=.*', spack_f77, 'Makefile')
+        filter_file(r'^FC\s*=.*',  spack_fc,  'Makefile')
+
   #. Replacing ``#!/usr/bin/perl`` with ``#!/usr/bin/env perl`` in ``bib2xhtml``:
 
      .. code-block:: python
@@ -2221,6 +2625,59 @@ File functions
 
 .. _package-lifecycle:
 
+Coding Style Guidelines
+---------------------------
+
+The following guidelines are provided, in the interests of making
+Spack packages work in a consistent manner:
+
+
+Variant Names
+~~~~~~~~~~~~~~
+
+Spack packages with variants similar to already-existing Spack
+packages should use the same name for their variants.  Standard
+variant names are:
+
+  ======= ======== ========================
+  Name    Default   Description
+  ======= ======== ========================
+  shared   True     Build shared libraries
+  static            Build static libraries
+  mpi               Use MPI
+  python            Build Python extension
+  ======= ======== ========================
+
+If specified in this table, the corresponding default should be used
+when declaring a variant.
+
+
+Version Lists
+~~~~~~~~~~~~~~
+
+Spack packges should list supported versions with the newest first.
+
+Special Versions
+~~~~~~~~~~~~~~~~~
+
+The following *special* version names may be used when building a package:
+
+* *@system*: Indicates a hook to the OS-installed version of the
+   package.  This is useful, for example, to tell Spack to use the
+   OS-installed version in ``packages.yaml``::
+
+        openssl:
+            paths:
+                openssl@system: /usr
+            buildable: False
+
+   Certain Spack internals look for the *@system* version and do
+   appropriate things in that case.
+
+* *@local*: Indicates the version was built manually from some source
+  tree of unknown provenance (see ``spack setup``).
+
+
 Packaging workflow commands
 ---------------------------------
 
@@ -2315,11 +2772,16 @@ build process will start from scratch.
 
 ``spack purge``
 ~~~~~~~~~~~~~~~~~
-Cleans up all of Spack's temporary files.  Use this to recover disk
-space if temporary files from interrupted or failed installs
-accumulate in the staging area.  This is equivalent to running ``spack
-clean`` for every package you have fetched or staged.
+Cleans up all of Spack's temporary and cached files.  This can be used to
+recover disk space if temporary files from interrupted or failed installs
+accumulate in the staging area.
 
+When called with ``--stage`` or ``--all`` (or without arguments, in which case
+the default is ``--all``) this removes all staged files; this is equivalent to
+running ``spack clean`` for every package you have fetched or staged.
+
+When called with ``--cache`` or ``--all`` this will clear all resources
+:ref:`cached <caching>` during installs.
 
 Keeping the stage directory on success
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -2467,11 +2929,11 @@ build it:
    $ spack stage libelf
    ==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.13.tar.gz
    ######################################################################## 100.0%
-   ==> Staging archive: /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3=linux-ppc64/libelf-0.8.13.tar.gz
-   ==> Created stage in /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3=linux-ppc64.
+   ==> Staging archive: /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-debian7-x86_64/libelf-0.8.13.tar.gz
+   ==> Created stage in /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-debian7-x86_64.
    $ spack cd libelf
    $ pwd
-   /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3=linux-ppc64/libelf-0.8.13
+   /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3 arch=linux-debian7-x86_64/libelf-0.8.13
 
 ``spack cd`` here changed he current working directory to the
 directory containing the expanded ``libelf`` source code.  There are a
@@ -2536,3 +2998,4 @@ might write:
    DWARF_PREFIX = $(spack location -i libdwarf)
    CXXFLAGS += -I$DWARF_PREFIX/include
    CXXFLAGS += -L$DWARF_PREFIX/lib
+

lib/spack/docs/site_configuration.rst

@@ -1,186 +0,0 @@
-.. _site-configuration:
-
-Site configuration
-===================================
-
-.. _temp-space:
-
-Temporary space
-----------------------------
-
-.. warning:: Temporary space configuration will be moved to configuration files.
-   The instructions here are old and refer to ``__init__.py``
-
-By default, Spack will try to do all of its building in temporary
-space.  There are two main reasons for this.  First, Spack is designed
-to run out of a user's home directory, and on may systems the home
-directory is network mounted and potentially not a very fast
-filesystem.  We create build stages in a temporary directory to avoid
-this.  Second, many systems impose quotas on home directories, and
-``/tmp`` or similar directories often have more available space.  This
-helps conserve space for installations in users' home directories.
-
-You can customize temporary directories by editing
-``lib/spack/spack/__init__.py``.  Specifically, find this part of the file:
-
-.. code-block:: python
-
-   # Whether to build in tmp space or directly in the stage_path.
-   # If this is true, then spack will make stage directories in
-   # a tmp filesystem, and it will symlink them into stage_path.
-   use_tmp_stage = True
-
-   # Locations to use for staging and building, in order of preference
-   # Use a %u to add a username to the stage paths here, in case this
-   # is a shared filesystem.  Spack will use the first of these paths
-   # that it can create.
-   tmp_dirs = ['/nfs/tmp2/%u/spack-stage',
-               '/var/tmp/%u/spack-stage',
-               '/tmp/%u/spack-stage']
-
-The ``use_tmp_stage`` variable controls whether Spack builds
-**directly** inside the ``var/spack/`` directory.  Normally, Spack
-will try to find a temporary directory for a build, then it *symlinks*
-that temporary directory into ``var/spack/`` so that you can keep
-track of what temporary directories Spack is using.
-
-The ``tmp_dirs`` variable is a list of paths Spack should search when
-trying to find a temporary directory.  They can optionally contain a
-``%u``, which will substitute the current user's name into the path.
-The list is searched in order, and Spack will create a temporary stage
-in the first directory it finds to which it has write access.  Add
-more elements to the list to indicate where your own site's temporary
-directory is.
-
-
-.. _concretization-policies:
-
-Concretization policies
-----------------------------
-
-When a user asks for a package like ``mpileaks`` to be installed,
-Spack has to make decisions like what version should be installed,
-what compiler to use, and how its dependencies should be configured.
-This process is called *concretization*, and it's covered in detail in
-:ref:`its own section <abstract-and-concrete>`.
-
-The default concretization policies are in the
-:py:mod:`spack.concretize` module, specifically in the
-:py:class:`spack.concretize.DefaultConcretizer` class.  These are the
-important methods used in the concretization process:
-
-* :py:meth:`concretize_version(self, spec) <spack.concretize.DefaultConcretizer.concretize_version>`
-* :py:meth:`concretize_architecture(self, spec) <spack.concretize.DefaultConcretizer.concretize_architecture>`
-* :py:meth:`concretize_compiler(self, spec) <spack.concretize.DefaultConcretizer.concretize_compiler>`
-* :py:meth:`choose_provider(self, spec, providers) <spack.concretize.DefaultConcretizer.choose_provider>`
-
-The first three take a :py:class:`Spec <spack.spec.Spec>` object and
-modify it by adding constraints for the version.  For example, if the
-input spec had a version range like `1.0:5.0.3`, then the
-``concretize_version`` method should set the spec's version to a
-*single* version in that range.  Likewise, ``concretize_architecture``
-selects an architecture when the input spec does not have one, and
-``concretize_compiler`` needs to set both a concrete compiler and a
-concrete compiler version.
-
-``choose_provider()`` affects how concrete implementations are chosen
-based on a virtual dependency spec.  The input spec is some virtual
-dependency and the ``providers`` index is a :py:class:`ProviderIndex
-<spack.packages.ProviderIndex>` object.  The ``ProviderIndex`` maps
-the virtual spec to specs for possible implementations, and
-``choose_provider()`` should simply choose one of these.  The
-``concretize_*`` methods will be called on the chosen implementation
-later, so there is no need to fully concretize the spec when returning
-it.
-
-The ``DefaultConcretizer`` is intended to provide sensible defaults
-for each policy, but there are certain choices that it can't know
-about.  For example, one site might prefer ``OpenMPI`` over ``MPICH``,
-or another might prefer an old version of some packages.  These types
-of special cases can be integrated with custom concretizers.
-
-Writing a custom concretizer
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-To write your own concretizer, you need only subclass
-``DefaultConcretizer`` and override the methods you want to change.
-For example, you might write a class like this to change *only* the
-``concretize_version()`` behavior:
-
-.. code-block:: python
-
-   from spack.concretize import DefaultConcretizer
-
-   class MyConcretizer(DefaultConcretizer):
-       def concretize_version(self, spec):
-           # implement custom logic here.
-
-Once you have written your custom concretizer, you can make Spack use
-it by editing ``globals.py``.  Find this part of the file:
-
-.. code-block:: python
-
-   #
-   # This controls how things are concretized in spack.
-   # Replace it with a subclass if you want different
-   # policies.
-   #
-   concretizer = DefaultConcretizer()
-
-Set concretizer to *your own* class instead of the default:
-
-.. code-block:: python
-
-   concretizer = MyConcretizer()
-
-The next time you run Spack, your changes should take effect.
-
-
-Profiling
-~~~~~~~~~~~~~~~~~~~~~
-
-Spack has some limited built-in support for profiling, and can report
-statistics using standard Python timing tools.  To use this feature,
-supply ``-p`` to Spack on the command line, before any subcommands.
-
-.. _spack-p:
-
-``spack -p``
-^^^^^^^^^^^^^^^^^^
-
-``spack -p`` output looks like this:
-
-.. code-block:: sh
-
-   $ spack -p graph dyninst
-   o  dyninst
-   |\
-   | |\
-   | o |  libdwarf
-   |/ /
-   o |  libelf
-    /
-   o  boost
-
-         307670 function calls (305943 primitive calls) in 0.127 seconds
-
-   Ordered by: internal time
-
-   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
-      853    0.021    0.000    0.066    0.000 inspect.py:472(getmodule)
-    51197    0.011    0.000    0.018    0.000 inspect.py:51(ismodule)
-    73961    0.010    0.000    0.010    0.000 {isinstance}
-     1762    0.006    0.000    0.053    0.000 inspect.py:440(getsourcefile)
-    32075    0.006    0.000    0.006    0.000 {hasattr}
-     1760    0.004    0.000    0.004    0.000 {posix.stat}
-     2240    0.004    0.000    0.004    0.000 {posix.lstat}
-     2602    0.004    0.000    0.011    0.000 inspect.py:398(getfile)
-      771    0.004    0.000    0.077    0.000 inspect.py:518(findsource)
-     2656    0.004    0.000    0.004    0.000 {method 'match' of '_sre.SRE_Pattern' objects}
-    30772    0.003    0.000    0.003    0.000 {method 'get' of 'dict' objects}
-    ...
-
-The bottom of the output shows the top most time consuming functions,
-slowest on top.  The profiling support is from Python's built-in tool,
-`cProfile
-<https://docs.python.org/2/library/profile.html#module-cProfile>`_.

lib/spack/docs/spack_workflows.rst

@@ -0,0 +1,576 @@
+Spack Workflows
+===============================
+
+The process of using Spack involves building packages, running
+binaries from those packages, and developing software that depends on
+those packages.  For example, one might use Spack to build the
+`netcdf` package, use `spack load` to run the `ncdump` binary, and
+finally, write a small C program to read/write a particular NetCDF file.
+
+Spack supports a variety of workflows to suit a variety of situaions
+and user preferences, there is no single way to do all these things.
+This chapter demonstrates different workflows that have been
+developed, pointing out the pros and cons of them.
+
+
+Definitions
+############
+
+First some basic definitions.
+
+Package, Concrete Spec, Installed Package
+------------------------------------------
+
+In Spack, a package is an abstract recipe to build one piece of software.
+Spack packages may be used to build, in principle, any version of that
+software with any set of variants.  Examples of packages include
+``curl`` and ``zlib``.
+
+A package may be *instantiated* to produce a concrete spec; one
+possible realization of a particular package, out of combinatorially
+many other realizations.  For example, here is a concrete spec
+instantiated from ``curl``:
+
+.. code-block:: sh
+
+    curl@7.50.1%gcc@5.3.0 arch=linux-SuSE11-x86_64
+        ^openssl@system%gcc@5.3.0 arch=linux-SuSE11-x86_64
+        ^zlib@1.2.8%gcc@5.3.0 arch=linux-SuSE11-x86_64
+
+Spack's core concretization algorithm generates concrete specs by
+instantiating packages from its repo, based on a set of "hints",
+including user input and the ``packages.yaml`` file.  This algorithm
+may be accessed at any time with the ``spack spec`` command.  For
+example:
+
+.. code-block:: sh
+
+    $ spack spec curl
+      curl@7.50.1%gcc@5.3.0 arch=linux-SuSE11-x86_64
+          ^openssl@system%gcc@5.3.0 arch=linux-SuSE11-x86_64
+          ^zlib@1.2.8%gcc@5.3.0 arch=linux-SuSE11-x86_64
+
+Every time Spack installs a package, that installation corresponds to
+a concrete spec.  Only a vanishingly small fraction of possible
+concrete specs will be installed at any one Spack site.
+
+Consistent Sets
+----------------
+
+A set of Spack specs is said to be *consistent* if each package is
+only instantiated one way within it --- that is, if two specs in the
+set have the same package, then they must also have the same version,
+variant, compiler, etc.  For example, the following set is consistent:
+
+.. code-block:: sh
+
+    curl@7.50.1%gcc@5.3.0 arch=linux-SuSE11-x86_64
+        ^openssl@system%gcc@5.3.0 arch=linux-SuSE11-x86_64
+        ^zlib@1.2.8%gcc@5.3.0 arch=linux-SuSE11-x86_64
+    zlib@1.2.8%gcc@5.3.0 arch=linux-SuSE11-x86_64
+
+The following set is not consistent:
+
+.. code-block:: sh
+
+    curl@7.50.1%gcc@5.3.0 arch=linux-SuSE11-x86_64
+        ^openssl@system%gcc@5.3.0 arch=linux-SuSE11-x86_64
+        ^zlib@1.2.8%gcc@5.3.0 arch=linux-SuSE11-x86_64
+    zlib@1.2.7%gcc@5.3.0 arch=linux-SuSE11-x86_64    
+
+The compatibility of a set of installed packages determines what may
+be done with it.  It is always possible to ``spack load`` any set of
+installed packages, whether or not they are consistent, and run their
+binaries from the command line.  However, a set of installed packages
+can only be linked together in one binary if it is consistent.
+
+If the user produces a series of `spack spec` or `spack load`
+commands, in general there is no guarantee of consistency between
+them.  Spack's concretization procedure guarantees that the results of
+any *single* `spack spec` call will be consistent.  Therefore, the
+best way to ensure a consistent set of specs is to create a Spack
+package with dependencies, and then instantiate that package.  We will
+use this technique below.
+
+
+Building Packages
+##################
+
+Suppose you are tasked with installing a set of software packages on a
+system in order to support one application -- both a core application
+program, plus software to prepare input and analyze output.  The
+required software might be summed up as a series of ``spack install``
+commands in a script.  If needed, this script can always be run again
+in the future.  For example:
+
+.. code-block::
+
+    spack install modele-utils
+    spack install emacs
+    spack install ncview
+    spack install nco
+    spack install modele-control
+    spack install py-numpy
+
+In most cases, this script will not correctly install software
+according to your specific needs: choices need to be made for
+variants, versions and virtual dependency choices may be needed.  It
+*is* possible to specify these choices by extending specs on the
+command line; however, the same choices must be specified repeatedly.
+For example, if you wish to use ``openmpi`` to satisfy the ``mpi``
+dependency, then ``^openmpi`` will have to appear on *every* ``spack
+install`` line that uses MPI.  It can get repetitve fast.
+
+Custimizing Spack installation options is easier to do in the
+``~/.spack/packages.yaml`` file.  In this file, you can specify
+preferred versions and variants to use for packages.  For exmaple:
+
+.. code-block:: yaml
+
+    packages:
+        python:
+            version: [3.5.1]
+        modele-utils:
+            version: [cmake]
+
+        everytrace:
+            version: [develop]
+        eigen:
+            variants: ~suitesparse
+        netcdf:
+            variants: +mpi
+
+        all:
+            compiler: [gcc@5.3.0]
+            providers:
+                mpi: [openmpi]
+                blas: [openblas]
+                lapack: [openblas]
+
+
+This approach will work as long as you are building packages for just
+one application.  
+
+Multiple Applications
+-----------------------
+
+Suppose instead you're building multiple inconsistent applications.
+For example, users want package A to be built with ``openmpi`` and
+package B with ``mpich`` --- but still share many other lower-level
+dependencies.  In this case, a single ``packages.yaml`` file will not
+work.  Plans are to implement *per-project* ``packages.yaml`` files.
+In the meantime, one could write shell scripts to switch
+``packages.yaml`` between multiple versions as needed, using symlinks.
+
+
+Combinatorial Sets
+--------------------------
+
+Suppose that you are now tasked with systematically building many
+incompatible versions of packages.  For example, you need to build
+``petsc`` 9 times for 3 different MPI implementations on 3 different
+compilers, in order to support user needs.  In this case, you will
+need to either create 9 different ``packages.yaml`` files; or more
+likely, create 9 different ``spack install`` command lines with the
+correct options in the spec.
+
+
+
+Loading Packages
+#################
+
+Once Spack packages have been built, the next step is to use them.  As
+with buiding packages, there are many ways to use them, depending on
+the use case.
+
+Simple Loads
+--------------
+
+Suppose that Spack has been used to install a set of command-line
+programs, which users now wish to use.  One can in principle put a
+number of ``spack load`` commands into ``.bashrc``, for example:
+
+.. code-block::
+
+    spack load modele-utils
+    spack load emacs
+    spack load ncview
+    spack load nco
+    spack load modele-control
+
+Although simple load scripts like this are useful in many cases, the
+have some drawbacks:
+
+1. The set of modules loaded by them will in general not be
+   consistent.  They are a decent way to load commands to be called
+   from command shells.  See below for better ways to assemble a
+   consistent set of packages for building application programs.
+
+2. The ``spack spec`` and ``spack install`` commands use a
+   sophisticated concretization algorithm that chooses the "best"
+   among several options, taking into account ``packages.yaml`` file.
+   The ``spack load`` and ``spack module loads`` commands, on the
+   other thand, are not very smart: if the user-supplied spec matches
+   more than one installed package, then ``spack module loads`` will
+   fail. This may change in the future.  For now, the workaround is to
+   be more specific on any ``spack module loads`` lines that fail.
+
+
+Cached Simple Loads
+----------------------
+
+Anoter problem with using `spack load` is, it is slow; a typical user
+environment could take several seconds to load, and would not be
+appropriate to put into ``.bashrc`` directly.  It is preferable to use
+a series of ``spack module loads`` commands to pre-compute which
+modules to load.  These can be put in a script that is run whenever
+installed Spack packages change.  For example:
+
+.. code-block:: sh
+    #!/bin/sh
+    #
+    # Generate module load commands in ~/env/spackenv
+
+    cat <<EOF | /bin/sh >$HOME/env/spackenv
+    FIND='spack module loads --prefix linux-SuSE11-x86_64/'
+
+    \$FIND modele-utils
+    \$FIND emacs
+    \$FIND ncview
+    \$FIND nco
+    \$FIND modele-control
+    EOF
+
+The output of this file is written in ``~/env/spackenv``:
+
+.. code-block:: sh
+
+    # binutils@2.25%gcc@5.3.0+gold~krellpatch~libiberty arch=linux-SuSE11-x86_64
+    module load linux-SuSE11-x86_64/binutils-2.25-gcc-5.3.0-6w5d2t4
+    # python@2.7.12%gcc@5.3.0~tk~ucs4 arch=linux-SuSE11-x86_64
+    module load linux-SuSE11-x86_64/python-2.7.12-gcc-5.3.0-2azoju2
+    # ncview@2.1.7%gcc@5.3.0 arch=linux-SuSE11-x86_64
+    module load linux-SuSE11-x86_64/ncview-2.1.7-gcc-5.3.0-uw3knq2
+    # nco@4.5.5%gcc@5.3.0 arch=linux-SuSE11-x86_64
+    module load linux-SuSE11-x86_64/nco-4.5.5-gcc-5.3.0-7aqmimu
+    # modele-control@develop%gcc@5.3.0 arch=linux-SuSE11-x86_64
+    module load linux-SuSE11-x86_64/modele-control-develop-gcc-5.3.0-7rddsij
+    # zlib@1.2.8%gcc@5.3.0 arch=linux-SuSE11-x86_64
+    module load linux-SuSE11-x86_64/zlib-1.2.8-gcc-5.3.0-fe5onbi
+    # curl@7.50.1%gcc@5.3.0 arch=linux-SuSE11-x86_64
+    module load linux-SuSE11-x86_64/curl-7.50.1-gcc-5.3.0-4vlev55
+    # hdf5@1.10.0-patch1%gcc@5.3.0+cxx~debug+fortran+mpi+shared~szip~threadsafe arch=linux-SuSE11-x86_64
+    module load linux-SuSE11-x86_64/hdf5-1.10.0-patch1-gcc-5.3.0-pwnsr4w
+    # netcdf@4.4.1%gcc@5.3.0~hdf4+mpi arch=linux-SuSE11-x86_64
+    module load linux-SuSE11-x86_64/netcdf-4.4.1-gcc-5.3.0-rl5canv
+    # netcdf-fortran@4.4.4%gcc@5.3.0 arch=linux-SuSE11-x86_64
+    module load linux-SuSE11-x86_64/netcdf-fortran-4.4.4-gcc-5.3.0-stdk2xq
+    # modele-utils@cmake%gcc@5.3.0+aux+diags+ic arch=linux-SuSE11-x86_64
+    module load linux-SuSE11-x86_64/modele-utils-cmake-gcc-5.3.0-idyjul5
+    # everytrace@develop%gcc@5.3.0+fortran+mpi arch=linux-SuSE11-x86_64
+    module load linux-SuSE11-x86_64/everytrace-develop-gcc-5.3.0-p5wmb25
+
+Users may now put ``source ~/env/spackenv`` into ``.bashrc``.
+
+.. note ::
+
+    Some module systems put a prefix on the names of modules created
+    by Spack.  For example, that prefix is ``linux-SuSE11-x86_64/`` in
+    the above case.  If a prefix is not needed, you may omit the
+    ``--prefix`` flag from ``spack module loads``.
+
+
+Transitive Dependencies
+---------------------------
+
+In the script above, each ``spack module loads`` command generates a
+*single* ``module load`` line.  Transitive dependencies do not usually
+need to be load, only modules the user needs in in ``$PATH``.  This is
+because Spack builds binaries with RPATH.  Spack's RPATH policy has
+some nice features:
+
+ 1. Modules for multiple inconsistent applications may be loaded
+    simultaneously.  In the above example (Multiple Applications),
+    package A and package B can coexist together in the user's $PATH,
+    even though they use different MPIs.
+
+ 2. RPATH eliminates a whole class of strange errors that can happen
+    in non-RPATH binaries when the wrong ``LD_LIBRARY_PATH`` is
+    loaded.
+
+ 3. Recursive module systems such as LMod are not necessary.
+
+ 4. Modules are not needed at all to execute binaries.  If a path to a
+    binary is known, it may be executed.  For example, the path for a
+    Spack-built compiler can be given to an IDE without requiring the
+    IDE to load that compiler's module.
+
+Unfortunately, Spacks' RPATH support does not work in all case.  For example:
+
+ 1. Software comes in many forms --- not just compiled ELF binaries,
+    but also as interpreted code in Python, R, JVM bytecode, etc.
+    Those systems almost universally use an environment variable
+    analogous to ``LD_LIBRARY_PATH`` to dynamically load libraries.
+
+ 2. Although Spack generally builds binaries with RPATH, it does not
+    currently do so for compiled Python extensions (for example,
+    ``py-numpy``).  Any libraries that these extensions depend on
+    (``openblas`` in this case, for example) must be specified in the
+    ``LD_LIBRARY_PATH``.`
+
+ 3. In some cases, Spack-generated binaries end up without a
+    functional RPATH for no discernable reason.
+
+In cases where RPATH support doesn't make things "just work," it can
+be necessary to load a module's dependencies as well as the module
+itself.  This is done by adding the ``--dependencies`` flag to the
+``spack module loads`` command.  For example, the following line,
+added to the script above, would be used to load Numpy, along with
+core Python, Setup TOols and a number of other packages:
+
+.. code-block:: sh
+    \$FIND --dependencies py-numpy
+
+Extension Packages
+---------------------
+
+Extensions (::ref:`packaging_extension` section) may be used as as an
+alternative to loading Python packages directly.  If extensions are
+activated, then ``spack load python`` will also load all the
+extensions activated for the given ``python``.  However, Spack
+extensions have two potential drawbacks:
+
+1. Activated packages that involve compiled C extensions may still
+   need their dependencies to be loaded manually.  For example,
+   ``spack load openblas`` might be required to make ``py-numpy``
+   work.
+
+2. Extensions "break" a core feature of Spack, which is that multiple
+   versions of a package can co-exist side-by-side.  For example,
+   suppose you wish to run a Python in two different environments but
+   the same basic Python --- one with ``py-numpy@1.7`` and one with
+   ``py-numpy@1.8``.  Spack extensions will not support this potential
+   debugging use case.
+
+
+
+Filesystem Views
+-------------------------------
+
+The above 
+
+.. Maybe this is not the right location for this documentation.
+
+The Spack installation area allows for many package installation trees
+to coexist and gives the user choices as to what versions and variants
+of packages to use.  To use them, the user must rely on a way to
+aggregate a subset of those packages.  The section on Environment
+Modules gives one good way to do that which relies on setting various
+environment variables.  An alternative way to aggregate is through
+**filesystem views**.
+
+A filesystem view is a single directory tree which is the union of the
+directory hierarchies of the individual package installation trees
+that have been included.  The files of the view's installed packages
+are brought into the view by symbolic or hard links back to their
+location in the original Spack installation area.  As the view is
+formed, any clashes due to a file having the exact same path in its
+package installation tree are handled in a first-come-first-served
+basis and a warning is printed.  Packages and their dependencies can
+be both added and removed.  During removal, empty directories will be
+purged.  These operations can be limited to pertain to just the
+packages listed by the user or to exclude specific dependencies and
+they allow for software installed outside of Spack to coexist inside
+the filesystem view tree.
+
+By its nature, a filesystem view represents a particular choice of one
+set of packages among all the versions and variants that are available
+in the Spack installation area.  It is thus equivalent to the
+directory hiearchy that might exist under ``/usr/local``.  While this
+limits a view to including only one version/variant of any package, it
+provides the benefits of having a simpler and traditional layout which
+may be used without any particular knowledge that its packages were
+built by Spack.
+
+Views can be used for a variety of purposes including:
+
+- A central installation in a traditional layout, eg ``/usr/local`` maintained over time by the sysadmin.
+- A self-contained installation area which may for the basis of a top-level atomic versioning scheme, eg ``/opt/pro`` vs ``/opt/dev``.
+- Providing an atomic and monolithic binary distribution, eg for delivery as a single tarball.
+- Producing ephemeral testing or developing environments.
+
+Using Filesystem Views
+~~~~~~~~~~~~~~~~~~~~~~
+
+A filesystem view is created and packages are linked in by the ``spack
+view`` command's ``symlink`` and ``hardlink`` sub-commands.  The
+``spack view remove`` command can be used to unlink some or all of the
+filesystem view.
+
+The following example creates a filesystem view based
+on an installed ``cmake`` package and then removes from the view the
+files in the ``cmake`` package while retaining its dependencies.
+
+.. code-block:: sh
+
+
+    $ spack view -v symlink myview cmake@3.5.2
+    ==> Linking package: "ncurses"
+    ==> Linking package: "zlib"
+    ==> Linking package: "openssl"
+    ==> Linking package: "cmake"
+
+    $ ls myview/
+    bin  doc  etc  include  lib  share
+
+    $ ls myview/bin/
+    captoinfo  clear  cpack     ctest    infotocap        openssl  tabs  toe   tset
+    ccmake     cmake  c_rehash  infocmp  ncurses6-config  reset    tic   tput
+
+    $ spack view -v -d false rm myview cmake@3.5.2
+    ==> Removing package: "cmake"
+
+    $ ls myview/bin/
+    captoinfo  c_rehash  infotocap        openssl  tabs  toe   tset
+    clear      infocmp   ncurses6-config  reset    tic   tput
+
+
+Limitations of Filesystem Views
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This section describes some limitations that should be considered in
+using filesystems views.
+
+Filesystem views are merely organizational.  The binary executable
+programs, shared libraries and other build products found in a view
+are mere links into the "real" Spack installation area.  If a view is
+built with symbolic links it requires the Spack-installed package to
+be kept in place.  Building a view with hardlinks removes this
+requirement but any internal paths (eg, rpath or ``#!`` interpreter
+specifications) will still require the Spack-installed package files
+to be in place.
+
+.. FIXME: reference the relocation work of Hegner and Gartung.
+
+As described above, when a view is built only a single instance of a
+file may exist in the unified filesystem tree.  If more than one
+package provides a file at the same path (relative to its own root)
+then it is the first package added to the view that "wins".  A warning
+is printed and it is up to the user to determine if the conflict
+matters.
+
+It is up to the user to assure a consistent view is produced.  In
+particular if the user excludes packages, limits the following of
+dependencies or removes packages the view may become inconsistent.  In
+particular, if two packages require the same sub-tree of dependencies,
+removing one package (recursively) will remove its dependencies and
+leave the other package broken.
+
+
+
+Build System Configuration Support
+----------------------------------
+
+Imagine a developer creating a CMake-based (or Autotools) project in a local
+directory, which depends on libraries A-Z.  Once Spack has installed
+those dependencies, one would like to run ``cmake`` with appropriate
+command line and environment so CMake can find them.  The ``spack
+setup`` command does this conveniently, producing a CMake
+configuration that is essentially the same as how Spack *would have*
+configured the project.  This can be demonstrated with a usage
+example:
+
+.. code-block:: bash
+
+   cd myproject
+    spack setup myproject@local
+    mkdir build; cd build
+    ../spconfig.py ..
+    make
+    make install
+
+Notes:
+  * Spack must have ``myproject/package.py`` in its repository for
+    this to work.
+  * ``spack setup`` produces the executable script ``spconfig.py`` in
+    the local directory, and also creates the module file for the
+    package.  ``spconfig.py`` is normally run from the user's
+    out-of-source build directory.
+  * The version number given to ``spack setup`` is arbitrary, just
+    like ``spack diy``.  ``myproject/package.py`` does not need to
+    have any valid downloadable versions listed (typical when a
+    project is new).
+  * spconfig.py produces a CMake configuration that *does not* use the
+    Spack wrappers.  Any resulting binaries *will not* use RPATH,
+    unless the user has enabled it.  This is recommended for
+    development purposes, not production.
+  * ``spconfig.py`` is human readable, and can serve as a developer
+    reference of what dependencies are being used.
+  * ``make install`` installs the package into the Spack repository,
+    where it may be used by other Spack packages.
+  * CMake-generated makefiles re-run CMake in some circumstances.  Use
+    of ``spconfig.py`` breaks this behavior, requiring the developer
+    to manually re-run ``spconfig.py`` when a ``CMakeLists.txt`` file
+    has changed.
+
+CMakePackage
+~~~~~~~~~~~~
+
+In order ot enable ``spack setup`` functionality, the author of
+``myproject/package.py`` must subclass from ``CMakePackage`` instead
+of the standard ``Package`` superclass.  Because CMake is
+standardized, the packager does not need to tell Spack how to run
+``cmake; make; make install``.  Instead the packager only needs to
+create (optional) methods ``configure_args()`` and ``configure_env()``, which
+provide the arguments (as a list) and extra environment variables (as
+a dict) to provide to the ``cmake`` command.  Usually, these will
+translate variant flags into CMake definitions.  For example:
+
+.. code-block:: python
+
+    def configure_args(self):
+        spec = self.spec
+        return [
+            '-DUSE_EVERYTRACE=%s' % ('YES' if '+everytrace' in spec else 'NO'),
+            '-DBUILD_PYTHON=%s' % ('YES' if '+python' in spec else 'NO'),
+            '-DBUILD_GRIDGEN=%s' % ('YES' if '+gridgen' in spec else 'NO'),
+            '-DBUILD_COUPLER=%s' % ('YES' if '+coupler' in spec else 'NO'),
+            '-DUSE_PISM=%s' % ('YES' if '+pism' in spec else 'NO')]
+
+If needed, a packager may also override methods defined in
+``StagedPackage`` (see below).
+
+
+StagedPackage
+~~~~~~~~~~~~~
+
+``CMakePackage`` is implemented by subclassing the ``StagedPackage``
+superclass, which breaks down the standard ``Package.install()``
+method into several sub-stages: ``setup``, ``configure``, ``build``
+and ``install``.  Details:
+
+* Instead of implementing the standard ``install()`` method, package
+  authors implement the methods for the sub-stages
+  ``install_setup()``, ``install_configure()``,
+  ``install_build()``, and ``install_install()``.
+
+* The ``spack install`` command runs the sub-stages ``configure``,
+  ``build`` and ``install`` in order.  (The ``setup`` stage is
+  not run by default; see below).
+* The ``spack setup`` command runs the sub-stages ``setup``
+  and a dummy install (to create the module file).
+* The sub-stage install methods take no arguments (other than
+  ``self``).  The arguments ``spec`` and ``prefix`` to the standard
+  ``install()`` method may be accessed via ``self.spec`` and
+  ``self.prefix``.
+
+GNU Autotools
+~~~~~~~~~~~~~
+
+The ``setup`` functionality is currently only available for
+CMake-based packages.  Extending this functionality to GNU
+Autotools-based packages would be easy (and should be done by a
+developer who actively uses Autotools).  Packages that use
+non-standard build systems can gain ``setup`` functionality by
+subclassing ``StagedPackage`` directly.
+

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://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
-# the Free Software Foundation) version 2.1 dated February 1999.
+# 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 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
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# 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
 ##############################################################################
 #
 # 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
-# the script runs.  They are set by routines in spack.build_environment
+# 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="
-SPACK_PREFIX
-SPACK_ENV_PATH
-SPACK_DEBUG_LOG_DIR
-SPACK_COMPILER_SPEC
-SPACK_SHORT_SPEC"
+parameters=(
+    SPACK_PREFIX
+    SPACK_ENV_PATH
+    SPACK_DEBUG_LOG_DIR
+    SPACK_COMPILER_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 $parameters; do
-    if [ -z "${!param}" ]; then
-        die "Spack compiler must be run from spack!  Input $param was missing!"
+for param in ${parameters[@]}; do
+    if [[ -z ${!param} ]]; then
+        die "Spack compiler must be run from Spack! Input '$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.
 #
@@ -78,33 +85,43 @@ done
 # 'command' is set based on the input command to $SPACK_[CC|CXX|F77|F90]
 #
 # 'mode' is set to one of:
+#    vcheck  version check
+#    cpp     preprocess
 #    cc      compile
+#    as      assemble
 #    ld      link
 #    ccld    compile & link
-#    cpp     preprocessor
-#    vcheck  version check
-#
+
 command=$(basename "$0")
+comp="CC"
 case "$command" in
-    cc|gcc|c89|c99|clang)
-        command="$SPACK_CC"
-        language="C"
-        ;;
-    c++|CC|g++|clang++)
-        command="$SPACK_CXX"
-        language="C++"
-        ;;
-    f77)
-        command="$SPACK_F77"
-        language="Fortran 77"
-        ;;
-    fc|f90|f95)
-        command="$SPACK_FC"
-        language="Fortran 90"
-        ;;
     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
+        ;;
+    ftn|f90|fc|f95|gfortran|ifort|pgfortran|xlf90|nagfor)
+        command="$SPACK_FC"
+        language="Fortran 90"
+        comp="FC"
+        lang_flags=F
+        ;;
+    f77|gfortran|ifort|pgfortran|xlf|nagfor|ftn)
+        command="$SPACK_F77"
+        language="Fortran 77"
+        comp="F77"
+        lang_flags=F
+        ;;
     ld)
         mode=ld
         ;;
@@ -113,179 +130,177 @@ case "$command" in
         ;;
 esac
 
-# Finish setting up the mode.
-if [ -z "$mode" ]; then
-    mode=ccld
+# If any of the arguments below are present, then the mode is vcheck.
+# In vcheck mode, nothing is added in terms of extra search paths or
+# libraries.
+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 || $arg == -dumpversion ]]; then
             mode=vcheck
             break
-        elif [ "$arg" = -E ]; then
+        fi
+    done
+fi
+
+# Finish setting up the mode.
+if [[ -z $mode ]]; then
+    mode=ccld
+    for arg in "$@"; do
+        if [[ $arg == -E ]]; then
             mode=cpp
             break
-        elif [ "$arg" = -c ]; then
+        elif [[ $arg == -S ]]; then
+            mode=as
+            break
+        elif [[ $arg == -c ]]; then
             mode=cc
             break
         fi
     done
 fi
 
-# Dump the version and exist if we're in testing mode.
-if [ "$SPACK_TEST_COMMAND" = "dump-mode" ]; then
+# Set up rpath variable according to language.
+eval rpath=\$SPACK_${comp}_RPATH_ARG
+
+# Dump the version and exit if we're in testing mode.
+if [[ $SPACK_TEST_COMMAND == dump-mode ]]; then
     echo "$mode"
     exit
 fi
 
 # Check that at least one of the real commands was actually selected,
 # otherwise we don't know what to execute.
-if [ -z "$command" ]; then
+if [[ -z $command ]]; then
     die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
 fi
 
+#
+# Filter '.' and Spack environment directories out of PATH so that
+# this script doesn't just call itself
+#
+IFS=':' read -ra env_path <<< "$PATH"
+IFS=':' read -ra spack_env_dirs <<< "$SPACK_ENV_PATH"
+spack_env_dirs+=("" ".")
+PATH=""
+for dir in "${env_path[@]}"; do
+    addpath=true
+    for env_dir in "${spack_env_dirs[@]}"; do
+        if [[ $dir == $env_dir ]]; then
+            addpath=false
+            break
+        fi
+    done
+    if $addpath; then
+        PATH="${PATH:+$PATH:}$dir"
+    fi
+done
+export PATH
+
+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=("$@")
 
-#
-# Now do real parsing of the command line args, trying hard to keep
-# non-rpath linker arguments in the proper order w.r.t. other command
-# line arguments.  This is important for things like groups.
-#
-includes=()
-libraries=()
-libs=()
-rpaths=()
-other_args=()
+# Prepend cppflags, cflags, cxxflags, fcflags, fflags, and ldflags
 
-while [ -n "$1" ]; do
-    case "$1" in
-        -I*)
-            arg="${1#-I}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            includes+=("$arg")
-            ;;
-        -L*)
-            arg="${1#-L}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libraries+=("$arg")
-            ;;
-        -l*)
-            arg="${1#-l}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libs+=("$arg")
-            ;;
-        -Wl,*)
-            arg="${1#-Wl,}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            if [[ "$arg" = -rpath=* ]]; then
-                rpaths+=("${arg#-rpath=}")
-            elif [[ "$arg" = -rpath ]]; then
-                shift; arg="$1"
-                if [[ "$arg" != -Wl,* ]]; then
-                    die "-Wl,-rpath was not followed by -Wl,*"
-                fi
-                rpaths+=("${arg#-Wl,}")
-            else
-                other_args+=("-Wl,$arg")
-            fi
-            ;;
-        -Xlinker,*)
-            arg="${1#-Xlinker,}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            if [[ "$arg" = -rpath=* ]]; then
-                rpaths+=("${arg#-rpath=}")
-            elif [[ "$arg" = -rpath ]]; then
-                shift; arg="$1"
-                if [[ "$arg" != -Xlinker,* ]]; then
-                    die "-Xlinker,-rpath was not followed by -Xlinker,*"
-                fi
-                rpaths+=("${arg#-Xlinker,}")
-            else
-                other_args+=("-Xlinker,$arg")
-            fi
-            ;;
-        *)
-            other_args+=("$1")
-            ;;
-    esac
-    shift
-done
+# Add ldflags
+case "$mode" in
+    ld|ccld)
+        args=(${SPACK_LDFLAGS[@]} "${args[@]}") ;;
+esac
 
-# Dump parsed values for unit testing if asked for
-if [ -n "$SPACK_TEST_COMMAND" ]; then
-    IFS=$'\n'
-    case "$SPACK_TEST_COMMAND" in
-        dump-includes)   echo "${includes[*]}";;
-        dump-libraries)  echo "${libraries[*]}";;
-        dump-libs)       echo "${libs[*]}";;
-        dump-rpaths)     echo "${rpaths[*]}";;
-        dump-other-args) echo "${other_args[*]}";;
-        dump-all)
-            echo "INCLUDES:"
-            echo "${includes[*]}"
-            echo
-            echo "LIBRARIES:"
-            echo "${libraries[*]}"
-            echo
-            echo "LIBS:"
-            echo "${libs[*]}"
-            echo
-            echo "RPATHS:"
-            echo "${rpaths[*]}"
-            echo
-            echo "ARGS:"
-            echo "${other_args[*]}"
-            ;;
-        *)
-            echo "ERROR: Unknown test command"
-            exit 1 ;;
-    esac
-    exit
-fi
+# Add compiler flags.
+case "$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
-    if [ -d "$dep/include" ]; then
-        includes+=("$dep/include")
+    # Prepend include directories
+    if [[ -d $dep/include ]]; then
+        if [[ $mode == cpp || $mode == cc || $mode == as || $mode == ccld ]]; then
+            args=("-I$dep/include" "${args[@]}")
+        fi
     fi
 
-    if [ -d "$dep/lib" ]; then
-        libraries+=("$dep/lib")
-        rpaths+=("$dep/lib")
+    # Prepend lib and RPATH directories
+    if [[ -d $dep/lib ]]; then
+        if [[ $mode == ccld ]]; then
+            $add_rpaths && args=("$rpath$dep/lib" "${args[@]}")
+            args=("-L$dep/lib" "${args[@]}")
+        elif [[ $mode == ld ]]; then
+            $add_rpaths && args=("-rpath" "$dep/lib" "${args[@]}")
+            args=("-L$dep/lib" "${args[@]}")
+        fi
     fi
 
-    if [ -d "$dep/lib64" ]; then
-        libraries+=("$dep/lib64")
-        rpaths+=("$dep/lib64")
+    # Prepend lib64 and RPATH directories
+    if [[ -d $dep/lib64 ]]; then
+        if [[ $mode == ccld ]]; then
+            $add_rpaths && args=("$rpath$dep/lib64" "${args[@]}")
+            args=("-L$dep/lib64" "${args[@]}")
+        elif [[ $mode == ld ]]; then
+            $add_rpaths && args=("-rpath" "$dep/lib64" "${args[@]}")
+            args=("-L$dep/lib64" "${args[@]}")
+        fi
     fi
 done
 
 # Include all -L's and prefix/whatever dirs in rpath
-for dir in "${libraries[@]}"; do
-    [ "$dir" != "." ] && rpaths+=("$dir")
-done
-rpaths+=("$SPACK_PREFIX/lib")
-rpaths+=("$SPACK_PREFIX/lib64")
-
-# Put the arguments together
-args=()
-for dir in "${includes[@]}";  do args+=("-I$dir"); done
-args+=("${other_args[@]}")
-for dir in "${libraries[@]}"; do args+=("-L$dir"); done
-for lib in "${libs[@]}";      do args+=("-l$lib"); done
-
-if [ "$mode" = ccld ]; then
-    for dir in "${rpaths[@]}"; do
-        args+=("-Wl,-rpath")
-        args+=("-Wl,$dir");
-    done
-elif [ "$mode" = ld ]; then
-    for dir in "${rpaths[@]}"; do
-        args+=("-rpath")
-        args+=("$dir");
-    done
+if [[ $mode == ccld ]]; then
+    $add_rpaths && args=("$rpath$SPACK_PREFIX/lib64" "${args[@]}")
+    $add_rpaths && args=("$rpath$SPACK_PREFIX/lib"   "${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.
 #
@@ -293,40 +308,24 @@ unset LD_LIBRARY_PATH
 unset LD_RUN_PATH
 unset DYLD_LIBRARY_PATH
 
-#
-# Filter '.' and Spack environment directories out of PATH so that
-# this script doesn't just call itself
-#
-IFS=':' read -ra env_path <<< "$PATH"
-IFS=':' read -ra spack_env_dirs <<< "$SPACK_ENV_PATH"
-spack_env_dirs+=(".")
-PATH=""
-for dir in "${env_path[@]}"; do
-    remove=""
-    for rm_dir in "${spack_env_dirs[@]}"; do
-        if [ "$dir" = "$rm_dir" ]; then remove=True; fi
-    done
-    if [ -z "$remove" ]; then
-        if [ -z "$PATH" ]; then
-            PATH="$dir"
-        else
-            PATH="$PATH:$dir"
-        fi
-    fi
-done
-export PATH
+full_command=("$command" "${args[@]}")
 
-full_command=("$command")
-full_command+=("${args[@]}")
+# In test command mode, write out full command for Spack tests.
+if [[ $SPACK_TEST_COMMAND == dump-args ]]; then
+    echo "${full_command[@]}"
+    exit
+elif [[ -n $SPACK_TEST_COMMAND ]]; then
+    die "ERROR: Unknown test command"
+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-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command"     >> $input_log
-    echo "$mode       ${full_command[@]}" >> $output_log
+    echo "[$mode] $command $input_command" >> "$input_log"
+    echo "[$mode] ${full_command[@]}" >> "$output_log"
 fi
 
 exec "${full_command[@]}"

lib/spack/env/clang

@@ -1 +0,0 @@
-cc

lib/spack/env/clang++

@@ -1 +0,0 @@
-cc

lib/spack/env/clang/clang

@@ -0,0 +1 @@
+../cc

lib/spack/env/clang/clang++

@@ -0,0 +1 @@
+../cc

lib/spack/env/cray/CC

@@ -0,0 +1 @@
+../cc

lib/spack/env/cray/cc

@@ -0,0 +1 @@
+../cc

lib/spack/env/cray/ftn

@@ -0,0 +1 @@
+../cc

lib/spack/env/craype/CC

@@ -0,0 +1 @@
+../cc

lib/spack/env/craype/cc

@@ -0,0 +1 @@
+../cc

lib/spack/env/craype/ftn

@@ -0,0 +1 @@
+../cc

lib/spack/env/g++

@@ -1 +0,0 @@
-cc

lib/spack/env/gcc

@@ -1 +0,0 @@
-cc

lib/spack/env/gcc/g++

@@ -0,0 +1 @@
+../cc

lib/spack/env/gcc/gcc

@@ -0,0 +1 @@
+../cc

lib/spack/env/gcc/gfortran

@@ -0,0 +1 @@
+../cc

lib/spack/env/intel/icc

@@ -0,0 +1 @@
+../cc

lib/spack/env/intel/icpc

@@ -0,0 +1 @@
+../cc

lib/spack/env/intel/ifort

@@ -0,0 +1 @@
+../cc

lib/spack/env/nag/nagfor

@@ -0,0 +1 @@
+../cc

lib/spack/env/pgi/pgc++

@@ -0,0 +1 @@
+../cc

lib/spack/env/pgi/pgcc

@@ -0,0 +1 @@
+../cc

lib/spack/env/pgi/pgfortran

@@ -0,0 +1 @@
+../cc

lib/spack/env/xl/xlc

@@ -0,0 +1 @@
+../cc

lib/spack/env/xl/xlc++

@@ -0,0 +1 @@
+../cc

lib/spack/env/xl/xlf

@@ -0,0 +1 @@
+../cc

lib/spack/env/xl/xlf90

@@ -0,0 +1 @@
+../cc

lib/spack/external/__init__.py

@@ -6,7 +6,7 @@
 # Written 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
@@ -28,6 +28,11 @@
 
 So far:
     argparse:    We include our own version to be Python 2.6 compatible.
-    pyqver2:     External script to query required python version of python source code.
-                 Used for ensuring 2.6 compatibility.
+
+    pyqver2:     External script to query required python version of
+                 python source code. Used for ensuring 2.6 compatibility.
+
+    functools:   Used for implementation of total_ordering.
+
+    yaml:        Used for config files.
 """

lib/spack/external/argparse.py

@@ -1067,9 +1067,13 @@ class _SubParsersAction(Action):
 
     class _ChoicesPseudoAction(Action):
 
-        def __init__(self, name, help):
+        def __init__(self, name, aliases, help):
+            metavar = dest = name
+            if aliases:
+                metavar += ' (%s)' % ', '.join(aliases)
             sup = super(_SubParsersAction._ChoicesPseudoAction, self)
-            sup.__init__(option_strings=[], dest=name, help=help)
+            sup.__init__(option_strings=[], dest=dest, help=help,
+                         metavar=metavar)
 
     def __init__(self,
                  option_strings,
@@ -1097,15 +1101,22 @@ def add_parser(self, name, **kwargs):
         if kwargs.get('prog') is None:
             kwargs['prog'] = '%s %s' % (self._prog_prefix, name)
 
+        aliases = kwargs.pop('aliases', ())
+
         # create a pseudo-action to hold the choice help
         if 'help' in kwargs:
             help = kwargs.pop('help')
-            choice_action = self._ChoicesPseudoAction(name, help)
+            choice_action = self._ChoicesPseudoAction(name, aliases, help)
             self._choices_actions.append(choice_action)
 
         # create the parser and add it to the map
         parser = self._parser_class(**kwargs)
         self._name_parser_map[name] = parser
+
+        # make parser available under aliases also
+        for alias in aliases:
+            self._name_parser_map[alias] = parser
+
         return parser
 
     def _get_subactions(self):
@@ -1123,8 +1134,9 @@ def __call__(self, parser, namespace, values, option_string=None):
         try:
             parser = self._name_parser_map[parser_name]
         except KeyError:
-            tup = parser_name, ', '.join(self._name_parser_map)
-            msg = _('unknown parser %r (choices: %s)' % tup)
+            args = {'parser_name': parser_name,
+                    'choices': ', '.join(self._name_parser_map)}
+            msg = _('unknown parser %(parser_name)r (choices: %(choices)s)') % args
             raise ArgumentError(self, msg)
 
         # parse all the remaining options into the namespace

lib/spack/external/jsonschema/COPYING

@@ -0,0 +1,19 @@
+Copyright (c) 2013 Julian Berman
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

lib/spack/external/jsonschema/README.rst

@@ -0,0 +1,104 @@
+==========
+jsonschema
+==========
+
+``jsonschema`` is an implementation of `JSON Schema <http://json-schema.org>`_
+for Python (supporting 2.6+ including Python 3).
+
+.. code-block:: python
+
+    >>> from jsonschema import validate
+
+    >>> # A sample schema, like what we'd get from json.load()
+    >>> schema = {
+    ...     "type" : "object",
+    ...     "properties" : {
+    ...         "price" : {"type" : "number"},
+    ...         "name" : {"type" : "string"},
+    ...     },
+    ... }
+
+    >>> # If no exception is raised by validate(), the instance is valid.
+    >>> validate({"name" : "Eggs", "price" : 34.99}, schema)
+
+    >>> validate(
+    ...     {"name" : "Eggs", "price" : "Invalid"}, schema
+    ... )                                   # doctest: +IGNORE_EXCEPTION_DETAIL
+    Traceback (most recent call last):
+        ...
+    ValidationError: 'Invalid' is not of type 'number'
+
+
+Features
+--------
+
+* Full support for
+  `Draft 3 <https://python-jsonschema.readthedocs.org/en/latest/validate/#jsonschema.Draft3Validator>`_
+  **and** `Draft 4 <https://python-jsonschema.readthedocs.org/en/latest/validate/#jsonschema.Draft4Validator>`_
+  of the schema.
+
+* `Lazy validation <https://python-jsonschema.readthedocs.org/en/latest/validate/#jsonschema.IValidator.iter_errors>`_
+  that can iteratively report *all* validation errors.
+
+* Small and extensible
+
+* `Programmatic querying <https://python-jsonschema.readthedocs.org/en/latest/errors/#module-jsonschema>`_
+  of which properties or items failed validation.
+
+
+Release Notes
+-------------
+
+* A simple CLI was added for validation
+* Validation errors now keep full absolute paths and absolute schema paths in
+  their ``absolute_path`` and ``absolute_schema_path`` attributes. The ``path``
+  and ``schema_path`` attributes are deprecated in favor of ``relative_path``
+  and ``relative_schema_path``\ .
+
+*Note:* Support for Python 3.2 was dropped in this release, and installation
+now uses setuptools.
+
+
+Running the Test Suite
+----------------------
+
+``jsonschema`` uses the wonderful `Tox <http://tox.readthedocs.org>`_ for its
+test suite. (It really is wonderful, if for some reason you haven't heard of
+it, you really should use it for your projects).
+
+Assuming you have ``tox`` installed (perhaps via ``pip install tox`` or your
+package manager), just run ``tox`` in the directory of your source checkout to
+run ``jsonschema``'s test suite on all of the versions of Python ``jsonschema``
+supports. Note that you'll need to have all of those versions installed in
+order to run the tests on each of them, otherwise ``tox`` will skip (and fail)
+the tests on that version.
+
+Of course you're also free to just run the tests on a single version with your
+favorite test runner. The tests live in the ``jsonschema.tests`` package.
+
+
+Community
+---------
+
+There's a `mailing list <https://groups.google.com/forum/#!forum/jsonschema>`_
+for this implementation on Google Groups.
+
+Please join, and feel free to send questions there.
+
+
+Contributing
+------------
+
+I'm Julian Berman.
+
+``jsonschema`` is on `GitHub <http://github.com/Julian/jsonschema>`_.
+
+Get in touch, via GitHub or otherwise, if you've got something to contribute,
+it'd be most welcome!
+
+You can also generally find me on Freenode (nick: ``tos9``) in various
+channels, including ``#python``.
+
+If you feel overwhelmingly grateful, you can woo me with beer money on
+`Gittip <https://www.gittip.com/Julian/>`_ or via Google Wallet with the email
+in my GitHub profile.

lib/spack/external/jsonschema/__init__.py

@@ -0,0 +1,26 @@
+"""
+An implementation of JSON Schema for Python
+
+The main functionality is provided by the validator classes for each of the
+supported JSON Schema versions.
+
+Most commonly, :func:`validate` is the quickest way to simply validate a given
+instance under a schema, and will create a validator for you.
+
+"""
+
+from jsonschema.exceptions import (
+    ErrorTree, FormatError, RefResolutionError, SchemaError, ValidationError
+)
+from jsonschema._format import (
+    FormatChecker, draft3_format_checker, draft4_format_checker,
+)
+from jsonschema.validators import (
+    Draft3Validator, Draft4Validator, RefResolver, validate
+)
+
+
+__version__ = "2.4.0"
+
+
+# flake8: noqa

lib/spack/external/jsonschema/__main__.py

@@ -0,0 +1,2 @@
+from jsonschema.cli import main
+main()

lib/spack/external/jsonschema/_format.py

@@ -0,0 +1,240 @@
+import datetime
+import re
+import socket
+
+from jsonschema.compat import str_types
+from jsonschema.exceptions import FormatError
+
+
+class FormatChecker(object):
+    """
+    A ``format`` property checker.
+
+    JSON Schema does not mandate that the ``format`` property actually do any
+    validation. If validation is desired however, instances of this class can
+    be hooked into validators to enable format validation.
+
+    :class:`FormatChecker` objects always return ``True`` when asked about
+    formats that they do not know how to validate.
+
+    To check a custom format using a function that takes an instance and
+    returns a ``bool``, use the :meth:`FormatChecker.checks` or
+    :meth:`FormatChecker.cls_checks` decorators.
+
+    :argument iterable formats: the known formats to validate. This argument
+                                can be used to limit which formats will be used
+                                during validation.
+
+    """
+
+    checkers = {}
+
+    def __init__(self, formats=None):
+        if formats is None:
+            self.checkers = self.checkers.copy()
+        else:
+            self.checkers = dict((k, self.checkers[k]) for k in formats)
+
+    def checks(self, format, raises=()):
+        """
+        Register a decorated function as validating a new format.
+
+        :argument str format: the format that the decorated function will check
+        :argument Exception raises: the exception(s) raised by the decorated
+            function when an invalid instance is found. The exception object
+            will be accessible as the :attr:`ValidationError.cause` attribute
+            of the resulting validation error.
+
+        """
+
+        def _checks(func):
+            self.checkers[format] = (func, raises)
+            return func
+        return _checks
+
+    cls_checks = classmethod(checks)
+
+    def check(self, instance, format):
+        """
+        Check whether the instance conforms to the given format.
+
+        :argument instance: the instance to check
+        :type: any primitive type (str, number, bool)
+        :argument str format: the format that instance should conform to
+        :raises: :exc:`FormatError` if instance does not conform to format
+
+        """
+
+        if format not in self.checkers:
+            return
+
+        func, raises = self.checkers[format]
+        result, cause = None, None
+        try:
+            result = func(instance)
+        except raises as e:
+            cause = e
+        if not result:
+            raise FormatError(
+                "%r is not a %r" % (instance, format), cause=cause,
+            )
+
+    def conforms(self, instance, format):
+        """
+        Check whether the instance conforms to the given format.
+
+        :argument instance: the instance to check
+        :type: any primitive type (str, number, bool)
+        :argument str format: the format that instance should conform to
+        :rtype: bool
+
+        """
+
+        try:
+            self.check(instance, format)
+        except FormatError:
+            return False
+        else:
+            return True
+
+
+_draft_checkers = {"draft3": [], "draft4": []}
+
+
+def _checks_drafts(both=None, draft3=None, draft4=None, raises=()):
+    draft3 = draft3 or both
+    draft4 = draft4 or both
+
+    def wrap(func):
+        if draft3:
+            _draft_checkers["draft3"].append(draft3)
+            func = FormatChecker.cls_checks(draft3, raises)(func)
+        if draft4:
+            _draft_checkers["draft4"].append(draft4)
+            func = FormatChecker.cls_checks(draft4, raises)(func)
+        return func
+    return wrap
+
+
+@_checks_drafts("email")
+def is_email(instance):
+    if not isinstance(instance, str_types):
+        return True
+    return "@" in instance
+
+
+_ipv4_re = re.compile(r"^\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3}$")
+
+@_checks_drafts(draft3="ip-address", draft4="ipv4")
+def is_ipv4(instance):
+    if not isinstance(instance, str_types):
+        return True
+    if not _ipv4_re.match(instance):
+        return False
+    return all(0 <= int(component) <= 255 for component in instance.split("."))
+
+
+if hasattr(socket, "inet_pton"):
+    @_checks_drafts("ipv6", raises=socket.error)
+    def is_ipv6(instance):
+        if not isinstance(instance, str_types):
+            return True
+        return socket.inet_pton(socket.AF_INET6, instance)
+
+
+_host_name_re = re.compile(r"^[A-Za-z0-9][A-Za-z0-9\.\-]{1,255}$")
+
+@_checks_drafts(draft3="host-name", draft4="hostname")
+def is_host_name(instance):
+    if not isinstance(instance, str_types):
+        return True
+    if not _host_name_re.match(instance):
+        return False
+    components = instance.split(".")
+    for component in components:
+        if len(component) > 63:
+            return False
+    return True
+
+
+try:
+    import rfc3987
+except ImportError:
+    pass
+else:
+    @_checks_drafts("uri", raises=ValueError)
+    def is_uri(instance):
+        if not isinstance(instance, str_types):
+            return True
+        return rfc3987.parse(instance, rule="URI")
+
+
+try:
+    import strict_rfc3339
+except ImportError:
+    try:
+        import isodate
+    except ImportError:
+        pass
+    else:
+        @_checks_drafts("date-time", raises=(ValueError, isodate.ISO8601Error))
+        def is_date(instance):
+            if not isinstance(instance, str_types):
+                return True
+            return isodate.parse_datetime(instance)
+else:
+        @_checks_drafts("date-time")
+        def is_date(instance):
+            if not isinstance(instance, str_types):
+                return True
+            return strict_rfc3339.validate_rfc3339(instance)
+
+
+@_checks_drafts("regex", raises=re.error)
+def is_regex(instance):
+    if not isinstance(instance, str_types):
+        return True
+    return re.compile(instance)
+
+
+@_checks_drafts(draft3="date", raises=ValueError)
+def is_date(instance):
+    if not isinstance(instance, str_types):
+        return True
+    return datetime.datetime.strptime(instance, "%Y-%m-%d")
+
+
+@_checks_drafts(draft3="time", raises=ValueError)
+def is_time(instance):
+    if not isinstance(instance, str_types):
+        return True
+    return datetime.datetime.strptime(instance, "%H:%M:%S")
+
+
+try:
+    import webcolors
+except ImportError:
+    pass
+else:
+    def is_css_color_code(instance):
+        return webcolors.normalize_hex(instance)
+
+
+    @_checks_drafts(draft3="color", raises=(ValueError, TypeError))
+    def is_css21_color(instance):
+        if (
+            not isinstance(instance, str_types) or
+            instance.lower() in webcolors.css21_names_to_hex
+        ):
+            return True
+        return is_css_color_code(instance)
+
+
+    def is_css3_color(instance):
+        if instance.lower() in webcolors.css3_names_to_hex:
+            return True
+        return is_css_color_code(instance)
+
+
+draft3_format_checker = FormatChecker(_draft_checkers["draft3"])
+draft4_format_checker = FormatChecker(_draft_checkers["draft4"])

lib/spack/external/jsonschema/_reflect.py

@@ -0,0 +1,155 @@
+# -*- test-case-name: twisted.test.test_reflect -*-
+# Copyright (c) Twisted Matrix Laboratories.
+# See LICENSE for details.
+
+"""
+Standardized versions of various cool and/or strange things that you can do
+with Python's reflection capabilities.
+"""
+
+import sys
+
+from jsonschema.compat import PY3
+
+
+class _NoModuleFound(Exception):
+    """
+    No module was found because none exists.
+    """
+
+
+
+class InvalidName(ValueError):
+    """
+    The given name is not a dot-separated list of Python objects.
+    """
+
+
+
+class ModuleNotFound(InvalidName):
+    """
+    The module associated with the given name doesn't exist and it can't be
+    imported.
+    """
+
+
+
+class ObjectNotFound(InvalidName):
+    """
+    The object associated with the given name doesn't exist and it can't be
+    imported.
+    """
+
+
+
+if PY3:
+    def reraise(exception, traceback):
+        raise exception.with_traceback(traceback)
+else:
+    exec("""def reraise(exception, traceback):
+        raise exception.__class__, exception, traceback""")
+
+reraise.__doc__ = """
+Re-raise an exception, with an optional traceback, in a way that is compatible
+with both Python 2 and Python 3.
+
+Note that on Python 3, re-raised exceptions will be mutated, with their
+C{__traceback__} attribute being set.
+
+@param exception: The exception instance.
+@param traceback: The traceback to use, or C{None} indicating a new traceback.
+"""
+
+
+def _importAndCheckStack(importName):
+    """
+    Import the given name as a module, then walk the stack to determine whether
+    the failure was the module not existing, or some code in the module (for
+    example a dependent import) failing.  This can be helpful to determine
+    whether any actual application code was run.  For example, to distiguish
+    administrative error (entering the wrong module name), from programmer
+    error (writing buggy code in a module that fails to import).
+
+    @param importName: The name of the module to import.
+    @type importName: C{str}
+    @raise Exception: if something bad happens.  This can be any type of
+        exception, since nobody knows what loading some arbitrary code might
+        do.
+    @raise _NoModuleFound: if no module was found.
+    """
+    try:
+        return __import__(importName)
+    except ImportError:
+        excType, excValue, excTraceback = sys.exc_info()
+        while excTraceback:
+            execName = excTraceback.tb_frame.f_globals["__name__"]
+            # in Python 2 execName is None when an ImportError is encountered,
+            # where in Python 3 execName is equal to the importName.
+            if execName is None or execName == importName:
+                reraise(excValue, excTraceback)
+            excTraceback = excTraceback.tb_next
+        raise _NoModuleFound()
+
+
+
+def namedAny(name):
+    """
+    Retrieve a Python object by its fully qualified name from the global Python
+    module namespace.  The first part of the name, that describes a module,
+    will be discovered and imported.  Each subsequent part of the name is
+    treated as the name of an attribute of the object specified by all of the
+    name which came before it.  For example, the fully-qualified name of this
+    object is 'twisted.python.reflect.namedAny'.
+
+    @type name: L{str}
+    @param name: The name of the object to return.
+
+    @raise InvalidName: If the name is an empty string, starts or ends with
+        a '.', or is otherwise syntactically incorrect.
+
+    @raise ModuleNotFound: If the name is syntactically correct but the
+        module it specifies cannot be imported because it does not appear to
+        exist.
+
+    @raise ObjectNotFound: If the name is syntactically correct, includes at
+        least one '.', but the module it specifies cannot be imported because
+        it does not appear to exist.
+
+    @raise AttributeError: If an attribute of an object along the way cannot be
+        accessed, or a module along the way is not found.
+
+    @return: the Python object identified by 'name'.
+    """
+    if not name:
+        raise InvalidName('Empty module name')
+
+    names = name.split('.')
+
+    # if the name starts or ends with a '.' or contains '..', the __import__
+    # will raise an 'Empty module name' error. This will provide a better error
+    # message.
+    if '' in names:
+        raise InvalidName(
+            "name must be a string giving a '.'-separated list of Python "
+            "identifiers, not %r" % (name,))
+
+    topLevelPackage = None
+    moduleNames = names[:]
+    while not topLevelPackage:
+        if moduleNames:
+            trialname = '.'.join(moduleNames)
+            try:
+                topLevelPackage = _importAndCheckStack(trialname)
+            except _NoModuleFound:
+                moduleNames.pop()
+        else:
+            if len(names) == 1:
+                raise ModuleNotFound("No module named %r" % (name,))
+            else:
+                raise ObjectNotFound('%r does not name an object' % (name,))
+
+    obj = topLevelPackage
+    for n in names[1:]:
+        obj = getattr(obj, n)
+
+    return obj

lib/spack/external/jsonschema/_utils.py

@@ -0,0 +1,213 @@
+import itertools
+import json
+import pkgutil
+import re
+
+from jsonschema.compat import str_types, MutableMapping, urlsplit
+
+
+class URIDict(MutableMapping):
+    """
+    Dictionary which uses normalized URIs as keys.
+
+    """
+
+    def normalize(self, uri):
+        return urlsplit(uri).geturl()
+
+    def __init__(self, *args, **kwargs):
+        self.store = dict()
+        self.store.update(*args, **kwargs)
+
+    def __getitem__(self, uri):
+        return self.store[self.normalize(uri)]
+
+    def __setitem__(self, uri, value):
+        self.store[self.normalize(uri)] = value
+
+    def __delitem__(self, uri):
+        del self.store[self.normalize(uri)]
+
+    def __iter__(self):
+        return iter(self.store)
+
+    def __len__(self):
+        return len(self.store)
+
+    def __repr__(self):
+        return repr(self.store)
+
+
+class Unset(object):
+    """
+    An as-of-yet unset attribute or unprovided default parameter.
+
+    """
+
+    def __repr__(self):
+        return "<unset>"
+
+
+def load_schema(name):
+    """
+    Load a schema from ./schemas/``name``.json and return it.
+
+    """
+
+    data = pkgutil.get_data(__package__, "schemas/{0}.json".format(name))
+    return json.loads(data.decode("utf-8"))
+
+
+def indent(string, times=1):
+    """
+    A dumb version of :func:`textwrap.indent` from Python 3.3.
+
+    """
+
+    return "\n".join(" " * (4 * times) + line for line in string.splitlines())
+
+
+def format_as_index(indices):
+    """
+    Construct a single string containing indexing operations for the indices.
+
+    For example, [1, 2, "foo"] -> [1][2]["foo"]
+
+    :type indices: sequence
+
+    """
+
+    if not indices:
+        return ""
+    return "[%s]" % "][".join(repr(index) for index in indices)
+
+
+def find_additional_properties(instance, schema):
+    """
+    Return the set of additional properties for the given ``instance``.
+
+    Weeds out properties that should have been validated by ``properties`` and
+    / or ``patternProperties``.
+
+    Assumes ``instance`` is dict-like already.
+
+    """
+
+    properties = schema.get("properties", {})
+    patterns = "|".join(schema.get("patternProperties", {}))
+    for property in instance:
+        if property not in properties:
+            if patterns and re.search(patterns, property):
+                continue
+            yield property
+
+
+def extras_msg(extras):
+    """
+    Create an error message for extra items or properties.
+
+    """
+
+    if len(extras) == 1:
+        verb = "was"
+    else:
+        verb = "were"
+    return ", ".join(repr(extra) for extra in extras), verb
+
+
+def types_msg(instance, types):
+    """
+    Create an error message for a failure to match the given types.
+
+    If the ``instance`` is an object and contains a ``name`` property, it will
+    be considered to be a description of that object and used as its type.
+
+    Otherwise the message is simply the reprs of the given ``types``.
+
+    """
+
+    reprs = []
+    for type in types:
+        try:
+            reprs.append(repr(type["name"]))
+        except Exception:
+            reprs.append(repr(type))
+    return "%r is not of type %s" % (instance, ", ".join(reprs))
+
+
+def flatten(suitable_for_isinstance):
+    """
+    isinstance() can accept a bunch of really annoying different types:
+        * a single type
+        * a tuple of types
+        * an arbitrary nested tree of tuples
+
+    Return a flattened tuple of the given argument.
+
+    """
+
+    types = set()
+
+    if not isinstance(suitable_for_isinstance, tuple):
+        suitable_for_isinstance = (suitable_for_isinstance,)
+    for thing in suitable_for_isinstance:
+        if isinstance(thing, tuple):
+            types.update(flatten(thing))
+        else:
+            types.add(thing)
+    return tuple(types)
+
+
+def ensure_list(thing):
+    """
+    Wrap ``thing`` in a list if it's a single str.
+
+    Otherwise, return it unchanged.
+
+    """
+
+    if isinstance(thing, str_types):
+        return [thing]
+    return thing
+
+
+def unbool(element, true=object(), false=object()):
+    """
+    A hack to make True and 1 and False and 0 unique for ``uniq``.
+
+    """
+
+    if element is True:
+        return true
+    elif element is False:
+        return false
+    return element
+
+
+def uniq(container):
+    """
+    Check if all of a container's elements are unique.
+
+    Successively tries first to rely that the elements are hashable, then
+    falls back on them being sortable, and finally falls back on brute
+    force.
+
+    """
+
+    try:
+        return len(set(unbool(i) for i in container)) == len(container)
+    except TypeError:
+        try:
+            sort = sorted(unbool(i) for i in container)
+            sliced = itertools.islice(sort, 1, None)
+            for i, j in zip(sort, sliced):
+                if i == j:
+                    return False
+        except (NotImplementedError, TypeError):
+            seen = []
+            for e in container:
+                e = unbool(e)
+                if e in seen:
+                    return False
+                seen.append(e)
+    return True

lib/spack/external/jsonschema/_validators.py

@@ -0,0 +1,358 @@
+import re
+
+from jsonschema import _utils
+from jsonschema.exceptions import FormatError, ValidationError
+from jsonschema.compat import iteritems
+
+
+FLOAT_TOLERANCE = 10 ** -15
+
+
+def patternProperties(validator, patternProperties, instance, schema):
+    if not validator.is_type(instance, "object"):
+        return
+
+    for pattern, subschema in iteritems(patternProperties):
+        for k, v in iteritems(instance):
+            if re.search(pattern, k):
+                for error in validator.descend(
+                    v, subschema, path=k, schema_path=pattern,
+                ):
+                    yield error
+
+
+def additionalProperties(validator, aP, instance, schema):
+    if not validator.is_type(instance, "object"):
+        return
+
+    extras = set(_utils.find_additional_properties(instance, schema))
+
+    if validator.is_type(aP, "object"):
+        for extra in extras:
+            for error in validator.descend(instance[extra], aP, path=extra):
+                yield error
+    elif not aP and extras:
+        error = "Additional properties are not allowed (%s %s unexpected)"
+        yield ValidationError(error % _utils.extras_msg(extras))
+
+
+def items(validator, items, instance, schema):
+    if not validator.is_type(instance, "array"):
+        return
+
+    if validator.is_type(items, "object"):
+        for index, item in enumerate(instance):
+            for error in validator.descend(item, items, path=index):
+                yield error
+    else:
+        for (index, item), subschema in zip(enumerate(instance), items):
+            for error in validator.descend(
+                item, subschema, path=index, schema_path=index,
+            ):
+                yield error
+
+
+def additionalItems(validator, aI, instance, schema):
+    if (
+        not validator.is_type(instance, "array") or
+        validator.is_type(schema.get("items", {}), "object")
+    ):
+        return
+
+    len_items = len(schema.get("items", []))
+    if validator.is_type(aI, "object"):
+        for index, item in enumerate(instance[len_items:], start=len_items):
+            for error in validator.descend(item, aI, path=index):
+                yield error
+    elif not aI and len(instance) > len(schema.get("items", [])):
+        error = "Additional items are not allowed (%s %s unexpected)"
+        yield ValidationError(
+            error %
+            _utils.extras_msg(instance[len(schema.get("items", [])):])
+        )
+
+
+def minimum(validator, minimum, instance, schema):
+    if not validator.is_type(instance, "number"):
+        return
+
+    if schema.get("exclusiveMinimum", False):
+        failed = float(instance) <= minimum
+        cmp = "less than or equal to"
+    else:
+        failed = float(instance) < minimum
+        cmp = "less than"
+
+    if failed:
+        yield ValidationError(
+            "%r is %s the minimum of %r" % (instance, cmp, minimum)
+        )
+
+
+def maximum(validator, maximum, instance, schema):
+    if not validator.is_type(instance, "number"):
+        return
+
+    if schema.get("exclusiveMaximum", False):
+        failed = instance >= maximum
+        cmp = "greater than or equal to"
+    else:
+        failed = instance > maximum
+        cmp = "greater than"
+
+    if failed:
+        yield ValidationError(
+            "%r is %s the maximum of %r" % (instance, cmp, maximum)
+        )
+
+
+def multipleOf(validator, dB, instance, schema):
+    if not validator.is_type(instance, "number"):
+        return
+
+    if isinstance(dB, float):
+        mod = instance % dB
+        failed = (mod > FLOAT_TOLERANCE) and (dB - mod) > FLOAT_TOLERANCE
+    else:
+        failed = instance % dB
+
+    if failed:
+        yield ValidationError("%r is not a multiple of %r" % (instance, dB))
+
+
+def minItems(validator, mI, instance, schema):
+    if validator.is_type(instance, "array") and len(instance) < mI:
+        yield ValidationError("%r is too short" % (instance,))
+
+
+def maxItems(validator, mI, instance, schema):
+    if validator.is_type(instance, "array") and len(instance) > mI:
+        yield ValidationError("%r is too long" % (instance,))
+
+
+def uniqueItems(validator, uI, instance, schema):
+    if (
+        uI and
+        validator.is_type(instance, "array") and
+        not _utils.uniq(instance)
+    ):
+        yield ValidationError("%r has non-unique elements" % instance)
+
+
+def pattern(validator, patrn, instance, schema):
+    if (
+        validator.is_type(instance, "string") and
+        not re.search(patrn, instance)
+    ):
+        yield ValidationError("%r does not match %r" % (instance, patrn))
+
+
+def format(validator, format, instance, schema):
+    if validator.format_checker is not None:
+        try:
+            validator.format_checker.check(instance, format)
+        except FormatError as error:
+            yield ValidationError(error.message, cause=error.cause)
+
+
+def minLength(validator, mL, instance, schema):
+    if validator.is_type(instance, "string") and len(instance) < mL:
+        yield ValidationError("%r is too short" % (instance,))
+
+
+def maxLength(validator, mL, instance, schema):
+    if validator.is_type(instance, "string") and len(instance) > mL:
+        yield ValidationError("%r is too long" % (instance,))
+
+
+def dependencies(validator, dependencies, instance, schema):
+    if not validator.is_type(instance, "object"):
+        return
+
+    for property, dependency in iteritems(dependencies):
+        if property not in instance:
+            continue
+
+        if validator.is_type(dependency, "object"):
+            for error in validator.descend(
+                instance, dependency, schema_path=property,
+            ):
+                yield error
+        else:
+            dependencies = _utils.ensure_list(dependency)
+            for dependency in dependencies:
+                if dependency not in instance:
+                    yield ValidationError(
+                        "%r is a dependency of %r" % (dependency, property)
+                    )
+
+
+def enum(validator, enums, instance, schema):
+    if instance not in enums:
+        yield ValidationError("%r is not one of %r" % (instance, enums))
+
+
+def ref(validator, ref, instance, schema):
+    with validator.resolver.resolving(ref) as resolved:
+        for error in validator.descend(instance, resolved):
+            yield error
+
+
+def type_draft3(validator, types, instance, schema):
+    types = _utils.ensure_list(types)
+
+    all_errors = []
+    for index, type in enumerate(types):
+        if type == "any":
+            return
+        if validator.is_type(type, "object"):
+            errors = list(validator.descend(instance, type, schema_path=index))
+            if not errors:
+                return
+            all_errors.extend(errors)
+        else:
+            if validator.is_type(instance, type):
+                return
+    else:
+        yield ValidationError(
+            _utils.types_msg(instance, types), context=all_errors,
+        )
+
+
+def properties_draft3(validator, properties, instance, schema):
+    if not validator.is_type(instance, "object"):
+        return
+
+    for property, subschema in iteritems(properties):
+        if property in instance:
+            for error in validator.descend(
+                instance[property],
+                subschema,
+                path=property,
+                schema_path=property,
+            ):
+                yield error
+        elif subschema.get("required", False):
+            error = ValidationError("%r is a required property" % property)
+            error._set(
+                validator="required",
+                validator_value=subschema["required"],
+                instance=instance,
+                schema=schema,
+            )
+            error.path.appendleft(property)
+            error.schema_path.extend([property, "required"])
+            yield error
+
+
+def disallow_draft3(validator, disallow, instance, schema):
+    for disallowed in _utils.ensure_list(disallow):
+        if validator.is_valid(instance, {"type" : [disallowed]}):
+            yield ValidationError(
+                "%r is disallowed for %r" % (disallowed, instance)
+            )
+
+
+def extends_draft3(validator, extends, instance, schema):
+    if validator.is_type(extends, "object"):
+        for error in validator.descend(instance, extends):
+            yield error
+        return
+    for index, subschema in enumerate(extends):
+        for error in validator.descend(instance, subschema, schema_path=index):
+            yield error
+
+
+def type_draft4(validator, types, instance, schema):
+    types = _utils.ensure_list(types)
+
+    if not any(validator.is_type(instance, type) for type in types):
+        yield ValidationError(_utils.types_msg(instance, types))
+
+
+def properties_draft4(validator, properties, instance, schema):
+    if not validator.is_type(instance, "object"):
+        return
+
+    for property, subschema in iteritems(properties):
+        if property in instance:
+            for error in validator.descend(
+                instance[property],
+                subschema,
+                path=property,
+                schema_path=property,
+            ):
+                yield error
+
+
+def required_draft4(validator, required, instance, schema):
+    if not validator.is_type(instance, "object"):
+        return
+    for property in required:
+        if property not in instance:
+            yield ValidationError("%r is a required property" % property)
+
+
+def minProperties_draft4(validator, mP, instance, schema):
+    if validator.is_type(instance, "object") and len(instance) < mP:
+        yield ValidationError(
+            "%r does not have enough properties" % (instance,)
+        )
+
+
+def maxProperties_draft4(validator, mP, instance, schema):
+    if not validator.is_type(instance, "object"):
+        return
+    if validator.is_type(instance, "object") and len(instance) > mP:
+        yield ValidationError("%r has too many properties" % (instance,))
+
+
+def allOf_draft4(validator, allOf, instance, schema):
+    for index, subschema in enumerate(allOf):
+        for error in validator.descend(instance, subschema, schema_path=index):
+            yield error
+
+
+def oneOf_draft4(validator, oneOf, instance, schema):
+    subschemas = enumerate(oneOf)
+    all_errors = []
+    for index, subschema in subschemas:
+        errs = list(validator.descend(instance, subschema, schema_path=index))
+        if not errs:
+            first_valid = subschema
+            break
+        all_errors.extend(errs)
+    else:
+        yield ValidationError(
+            "%r is not valid under any of the given schemas" % (instance,),
+            context=all_errors,
+        )
+
+    more_valid = [s for i, s in subschemas if validator.is_valid(instance, s)]
+    if more_valid:
+        more_valid.append(first_valid)
+        reprs = ", ".join(repr(schema) for schema in more_valid)
+        yield ValidationError(
+            "%r is valid under each of %s" % (instance, reprs)
+        )
+
+
+def anyOf_draft4(validator, anyOf, instance, schema):
+    all_errors = []
+    for index, subschema in enumerate(anyOf):
+        errs = list(validator.descend(instance, subschema, schema_path=index))
+        if not errs:
+            break
+        all_errors.extend(errs)
+    else:
+        yield ValidationError(
+            "%r is not valid under any of the given schemas" % (instance,),
+            context=all_errors,
+        )
+
+
+def not_draft4(validator, not_schema, instance, schema):
+    if validator.is_valid(instance, not_schema):
+        yield ValidationError(
+            "%r is not allowed for %r" % (not_schema, instance)
+        )

lib/spack/external/jsonschema/cli.py

@@ -0,0 +1,72 @@
+from __future__ import absolute_import
+import argparse
+import json
+import sys
+
+from jsonschema._reflect import namedAny
+from jsonschema.validators import validator_for
+
+
+def _namedAnyWithDefault(name):
+    if "." not in name:
+        name = "jsonschema." + name
+    return namedAny(name)
+
+
+def _json_file(path):
+    with open(path) as file:
+        return json.load(file)
+
+
+parser = argparse.ArgumentParser(
+    description="JSON Schema Validation CLI",
+)
+parser.add_argument(
+    "-i", "--instance",
+    action="append",
+    dest="instances",
+    type=_json_file,
+    help="a path to a JSON instance to validate "
+         "(may be specified multiple times)",
+)
+parser.add_argument(
+    "-F", "--error-format",
+    default="{error.instance}: {error.message}\n",
+    help="the format to use for each error output message, specified in "
+         "a form suitable for passing to str.format, which will be called "
+         "with 'error' for each error",
+)
+parser.add_argument(
+    "-V", "--validator",
+    type=_namedAnyWithDefault,
+    help="the fully qualified object name of a validator to use, or, for "
+         "validators that are registered with jsonschema, simply the name "
+         "of the class.",
+)
+parser.add_argument(
+    "schema",
+    help="the JSON Schema to validate with",
+    type=_json_file,
+)
+
+
+def parse_args(args):
+    arguments = vars(parser.parse_args(args=args or ["--help"]))
+    if arguments["validator"] is None:
+        arguments["validator"] = validator_for(arguments["schema"])
+    return arguments
+
+
+def main(args=sys.argv[1:]):
+    sys.exit(run(arguments=parse_args(args=args)))
+
+
+def run(arguments, stdout=sys.stdout, stderr=sys.stderr):
+    error_format = arguments["error_format"]
+    validator = arguments["validator"](schema=arguments["schema"])
+    errored = False
+    for instance in arguments["instances"] or ():
+        for error in validator.iter_errors(instance):
+            stderr.write(error_format.format(error=error))
+            errored = True
+    return errored

lib/spack/external/jsonschema/compat.py

@@ -0,0 +1,53 @@
+from __future__ import unicode_literals
+import sys
+import operator
+
+try:
+    from collections import MutableMapping, Sequence  # noqa
+except ImportError:
+    from collections.abc import MutableMapping, Sequence  # noqa
+
+PY3 = sys.version_info[0] >= 3
+
+if PY3:
+    zip = zip
+    from io import StringIO
+    from urllib.parse import (
+        unquote, urljoin, urlunsplit, SplitResult, urlsplit as _urlsplit
+    )
+    from urllib.request import urlopen
+    str_types = str,
+    int_types = int,
+    iteritems = operator.methodcaller("items")
+else:
+    from itertools import izip as zip  # noqa
+    from StringIO import StringIO
+    from urlparse import (
+        urljoin, urlunsplit, SplitResult, urlsplit as _urlsplit # noqa
+    )
+    from urllib import unquote  # noqa
+    from urllib2 import urlopen  # noqa
+    str_types = basestring
+    int_types = int, long
+    iteritems = operator.methodcaller("iteritems")
+
+
+# On python < 3.3 fragments are not handled properly with unknown schemes
+def urlsplit(url):
+    scheme, netloc, path, query, fragment = _urlsplit(url)
+    if "#" in path:
+        path, fragment = path.split("#", 1)
+    return SplitResult(scheme, netloc, path, query, fragment)
+
+
+def urldefrag(url):
+    if "#" in url:
+        s, n, p, q, frag = urlsplit(url)
+        defrag = urlunsplit((s, n, p, q, ''))
+    else:
+        defrag = url
+        frag = ''
+    return defrag, frag
+
+
+# flake8: noqa

lib/spack/external/jsonschema/exceptions.py

@@ -0,0 +1,264 @@
+from collections import defaultdict, deque
+import itertools
+import pprint
+import textwrap
+
+from jsonschema import _utils
+from jsonschema.compat import PY3, iteritems
+
+
+WEAK_MATCHES = frozenset(["anyOf", "oneOf"])
+STRONG_MATCHES = frozenset()
+
+_unset = _utils.Unset()
+
+
+class _Error(Exception):
+    def __init__(
+        self,
+        message,
+        validator=_unset,
+        path=(),
+        cause=None,
+        context=(),
+        validator_value=_unset,
+        instance=_unset,
+        schema=_unset,
+        schema_path=(),
+        parent=None,
+    ):
+        self.message = message
+        self.path = self.relative_path = deque(path)
+        self.schema_path = self.relative_schema_path = deque(schema_path)
+        self.context = list(context)
+        self.cause = self.__cause__ = cause
+        self.validator = validator
+        self.validator_value = validator_value
+        self.instance = instance
+        self.schema = schema
+        self.parent = parent
+
+        for error in context:
+            error.parent = self
+
+    def __repr__(self):
+        return "<%s: %r>" % (self.__class__.__name__, self.message)
+
+    def __str__(self):
+        return unicode(self).encode("utf-8")
+
+    def __unicode__(self):
+        essential_for_verbose = (
+            self.validator, self.validator_value, self.instance, self.schema,
+        )
+        if any(m is _unset for m in essential_for_verbose):
+            return self.message
+
+        pschema = pprint.pformat(self.schema, width=72)
+        pinstance = pprint.pformat(self.instance, width=72)
+        return self.message + textwrap.dedent("""
+
+            Failed validating %r in schema%s:
+            %s
+
+            On instance%s:
+            %s
+            """.rstrip()
+        ) % (
+            self.validator,
+            _utils.format_as_index(list(self.relative_schema_path)[:-1]),
+            _utils.indent(pschema),
+            _utils.format_as_index(self.relative_path),
+            _utils.indent(pinstance),
+        )
+
+    if PY3:
+        __str__ = __unicode__
+
+    @classmethod
+    def create_from(cls, other):
+        return cls(**other._contents())
+
+    @property
+    def absolute_path(self):
+        parent = self.parent
+        if parent is None:
+            return self.relative_path
+
+        path = deque(self.relative_path)
+        path.extendleft(parent.absolute_path)
+        return path
+
+    @property
+    def absolute_schema_path(self):
+        parent = self.parent
+        if parent is None:
+            return self.relative_schema_path
+
+        path = deque(self.relative_schema_path)
+        path.extendleft(parent.absolute_schema_path)
+        return path
+
+    def _set(self, **kwargs):
+        for k, v in iteritems(kwargs):
+            if getattr(self, k) is _unset:
+                setattr(self, k, v)
+
+    def _contents(self):
+        attrs = (
+            "message", "cause", "context", "validator", "validator_value",
+            "path", "schema_path", "instance", "schema", "parent",
+        )
+        return dict((attr, getattr(self, attr)) for attr in attrs)
+
+
+class ValidationError(_Error):
+    pass
+
+
+class SchemaError(_Error):
+    pass
+
+
+class RefResolutionError(Exception):
+    pass
+
+
+class UnknownType(Exception):
+    def __init__(self, type, instance, schema):
+        self.type = type
+        self.instance = instance
+        self.schema = schema
+
+    def __str__(self):
+        return unicode(self).encode("utf-8")
+
+    def __unicode__(self):
+        pschema = pprint.pformat(self.schema, width=72)
+        pinstance = pprint.pformat(self.instance, width=72)
+        return textwrap.dedent("""
+            Unknown type %r for validator with schema:
+            %s
+
+            While checking instance:
+            %s
+            """.rstrip()
+        ) % (self.type, _utils.indent(pschema), _utils.indent(pinstance))
+
+    if PY3:
+        __str__ = __unicode__
+
+
+
+class FormatError(Exception):
+    def __init__(self, message, cause=None):
+        super(FormatError, self).__init__(message, cause)
+        self.message = message
+        self.cause = self.__cause__ = cause
+
+    def __str__(self):
+        return self.message.encode("utf-8")
+
+    def __unicode__(self):
+        return self.message
+
+    if PY3:
+        __str__ = __unicode__
+
+
+class ErrorTree(object):
+    """
+    ErrorTrees make it easier to check which validations failed.
+
+    """
+
+    _instance = _unset
+
+    def __init__(self, errors=()):
+        self.errors = {}
+        self._contents = defaultdict(self.__class__)
+
+        for error in errors:
+            container = self
+            for element in error.path:
+                container = container[element]
+            container.errors[error.validator] = error
+
+            self._instance = error.instance
+
+    def __contains__(self, index):
+        """
+        Check whether ``instance[index]`` has any errors.
+
+        """
+
+        return index in self._contents
+
+    def __getitem__(self, index):
+        """
+        Retrieve the child tree one level down at the given ``index``.
+
+        If the index is not in the instance that this tree corresponds to and
+        is not known by this tree, whatever error would be raised by
+        ``instance.__getitem__`` will be propagated (usually this is some
+        subclass of :class:`LookupError`.
+
+        """
+
+        if self._instance is not _unset and index not in self:
+            self._instance[index]
+        return self._contents[index]
+
+    def __setitem__(self, index, value):
+        self._contents[index] = value
+
+    def __iter__(self):
+        """
+        Iterate (non-recursively) over the indices in the instance with errors.
+
+        """
+
+        return iter(self._contents)
+
+    def __len__(self):
+        """
+        Same as :attr:`total_errors`.
+
+        """
+
+        return self.total_errors
+
+    def __repr__(self):
+        return "<%s (%s total errors)>" % (self.__class__.__name__, len(self))
+
+    @property
+    def total_errors(self):
+        """
+        The total number of errors in the entire tree, including children.
+
+        """
+
+        child_errors = sum(len(tree) for _, tree in iteritems(self._contents))
+        return len(self.errors) + child_errors
+
+
+def by_relevance(weak=WEAK_MATCHES, strong=STRONG_MATCHES):
+    def relevance(error):
+        validator = error.validator
+        return -len(error.path), validator not in weak, validator in strong
+    return relevance
+
+
+relevance = by_relevance()
+
+
+def best_match(errors, key=relevance):
+    errors = iter(errors)
+    best = next(errors, None)
+    if best is None:
+        return
+    best = max(itertools.chain([best], errors), key=key)
+
+    while best.context:
+        best = min(best.context, key=key)
+    return best

lib/spack/external/jsonschema/schemas/draft3.json

@@ -0,0 +1,201 @@
+{
+    "$schema": "http://json-schema.org/draft-03/schema#",
+    "dependencies": {
+        "exclusiveMaximum": "maximum",
+        "exclusiveMinimum": "minimum"
+    },
+    "id": "http://json-schema.org/draft-03/schema#",
+    "properties": {
+        "$ref": {
+            "format": "uri",
+            "type": "string"
+        },
+        "$schema": {
+            "format": "uri",
+            "type": "string"
+        },
+        "additionalItems": {
+            "default": {},
+            "type": [
+                {
+                    "$ref": "#"
+                },
+                "boolean"
+            ]
+        },
+        "additionalProperties": {
+            "default": {},
+            "type": [
+                {
+                    "$ref": "#"
+                },
+                "boolean"
+            ]
+        },
+        "default": {
+            "type": "any"
+        },
+        "dependencies": {
+            "additionalProperties": {
+                "items": {
+                    "type": "string"
+                },
+                "type": [
+                    "string",
+                    "array",
+                    {
+                        "$ref": "#"
+                    }
+                ]
+            },
+            "default": {},
+            "type": [
+                "string",
+                "array",
+                "object"
+            ]
+        },
+        "description": {
+            "type": "string"
+        },
+        "disallow": {
+            "items": {
+                "type": [
+                    "string",
+                    {
+                        "$ref": "#"
+                    }
+                ]
+            },
+            "type": [
+                "string",
+                "array"
+            ],
+            "uniqueItems": true
+        },
+        "divisibleBy": {
+            "default": 1,
+            "exclusiveMinimum": true,
+            "minimum": 0,
+            "type": "number"
+        },
+        "enum": {
+            "minItems": 1,
+            "type": "array",
+            "uniqueItems": true
+        },
+        "exclusiveMaximum": {
+            "default": false,
+            "type": "boolean"
+        },
+        "exclusiveMinimum": {
+            "default": false,
+            "type": "boolean"
+        },
+        "extends": {
+            "default": {},
+            "items": {
+                "$ref": "#"
+            },
+            "type": [
+                {
+                    "$ref": "#"
+                },
+                "array"
+            ]
+        },
+        "format": {
+            "type": "string"
+        },
+        "id": {
+            "format": "uri",
+            "type": "string"
+        },
+        "items": {
+            "default": {},
+            "items": {
+                "$ref": "#"
+            },
+            "type": [
+                {
+                    "$ref": "#"
+                },
+                "array"
+            ]
+        },
+        "maxDecimal": {
+            "minimum": 0,
+            "type": "number"
+        },
+        "maxItems": {
+            "minimum": 0,
+            "type": "integer"
+        },
+        "maxLength": {
+            "type": "integer"
+        },
+        "maximum": {
+            "type": "number"
+        },
+        "minItems": {
+            "default": 0,
+            "minimum": 0,
+            "type": "integer"
+        },
+        "minLength": {
+            "default": 0,
+            "minimum": 0,
+            "type": "integer"
+        },
+        "minimum": {
+            "type": "number"
+        },
+        "pattern": {
+            "format": "regex",
+            "type": "string"
+        },
+        "patternProperties": {
+            "additionalProperties": {
+                "$ref": "#"
+            },
+            "default": {},
+            "type": "object"
+        },
+        "properties": {
+            "additionalProperties": {
+                "$ref": "#",
+                "type": "object"
+            },
+            "default": {},
+            "type": "object"
+        },
+        "required": {
+            "default": false,
+            "type": "boolean"
+        },
+        "title": {
+            "type": "string"
+        },
+        "type": {
+            "default": "any",
+            "items": {
+                "type": [
+                    "string",
+                    {
+                        "$ref": "#"
+                    }
+                ]
+            },
+            "type": [
+                "string",
+                "array"
+            ],
+            "uniqueItems": true
+        },
+        "uniqueItems": {
+            "default": false,
+            "type": "boolean"
+        }
+    },
+    "type": "object"
+}

lib/spack/external/jsonschema/schemas/draft4.json

@@ -0,0 +1,221 @@
+{
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "default": {},
+    "definitions": {
+        "positiveInteger": {
+            "minimum": 0,
+            "type": "integer"
+        },
+        "positiveIntegerDefault0": {
+            "allOf": [
+                {
+                    "$ref": "#/definitions/positiveInteger"
+                },
+                {
+                    "default": 0
+                }
+            ]
+        },
+        "schemaArray": {
+            "items": {
+                "$ref": "#"
+            },
+            "minItems": 1,
+            "type": "array"
+        },
+        "simpleTypes": {
+            "enum": [
+                "array",
+                "boolean",
+                "integer",
+                "null",
+                "number",
+                "object",
+                "string"
+            ]
+        },
+        "stringArray": {
+            "items": {
+                "type": "string"
+            },
+            "minItems": 1,
+            "type": "array",
+            "uniqueItems": true
+        }
+    },
+    "dependencies": {
+        "exclusiveMaximum": [
+            "maximum"
+        ],
+        "exclusiveMinimum": [
+            "minimum"
+        ]
+    },
+    "description": "Core schema meta-schema",
+    "id": "http://json-schema.org/draft-04/schema#",
+    "properties": {
+        "$schema": {
+            "format": "uri",
+            "type": "string"
+        },
+        "additionalItems": {
+            "anyOf": [
+                {
+                    "type": "boolean"
+                },
+                {
+                    "$ref": "#"
+                }
+            ],
+            "default": {}
+        },
+        "additionalProperties": {
+            "anyOf": [
+                {
+                    "type": "boolean"
+                },
+                {
+                    "$ref": "#"
+                }
+            ],
+            "default": {}
+        },
+        "allOf": {
+            "$ref": "#/definitions/schemaArray"
+        },
+        "anyOf": {
+            "$ref": "#/definitions/schemaArray"
+        },
+        "default": {},
+        "definitions": {
+            "additionalProperties": {
+                "$ref": "#"
+            },
+            "default": {},
+            "type": "object"
+        },
+        "dependencies": {
+            "additionalProperties": {
+                "anyOf": [
+                    {
+                        "$ref": "#"
+                    },
+                    {
+                        "$ref": "#/definitions/stringArray"
+                    }
+                ]
+            },
+            "type": "object"
+        },
+        "description": {
+            "type": "string"
+        },
+        "enum": {
+            "minItems": 1,
+            "type": "array",
+            "uniqueItems": true
+        },
+        "exclusiveMaximum": {
+            "default": false,
+            "type": "boolean"
+        },
+        "exclusiveMinimum": {
+            "default": false,
+            "type": "boolean"
+        },
+        "id": {
+            "format": "uri",
+            "type": "string"
+        },
+        "items": {
+            "anyOf": [
+                {
+                    "$ref": "#"
+                },
+                {
+                    "$ref": "#/definitions/schemaArray"
+                }
+            ],
+            "default": {}
+        },
+        "maxItems": {
+            "$ref": "#/definitions/positiveInteger"
+        },
+        "maxLength": {
+            "$ref": "#/definitions/positiveInteger"
+        },
+        "maxProperties": {
+            "$ref": "#/definitions/positiveInteger"
+        },
+        "maximum": {
+            "type": "number"
+        },
+        "minItems": {
+            "$ref": "#/definitions/positiveIntegerDefault0"
+        },
+        "minLength": {
+            "$ref": "#/definitions/positiveIntegerDefault0"
+        },
+        "minProperties": {
+            "$ref": "#/definitions/positiveIntegerDefault0"
+        },
+        "minimum": {
+            "type": "number"
+        },
+        "multipleOf": {
+            "exclusiveMinimum": true,
+            "minimum": 0,
+            "type": "number"
+        },
+        "not": {
+            "$ref": "#"
+        },
+        "oneOf": {
+            "$ref": "#/definitions/schemaArray"
+        },
+        "pattern": {
+            "format": "regex",
+            "type": "string"
+        },
+        "patternProperties": {
+            "additionalProperties": {
+                "$ref": "#"
+            },
+            "default": {},
+            "type": "object"
+        },
+        "properties": {
+            "additionalProperties": {
+                "$ref": "#"
+            },
+            "default": {},
+            "type": "object"
+        },
+        "required": {
+            "$ref": "#/definitions/stringArray"
+        },
+        "title": {
+            "type": "string"
+        },
+        "type": {
+            "anyOf": [
+                {
+                    "$ref": "#/definitions/simpleTypes"
+                },
+                {
+                    "items": {
+                        "$ref": "#/definitions/simpleTypes"
+                    },
+                    "minItems": 1,
+                    "type": "array",
+                    "uniqueItems": true
+                }
+            ]
+        },
+        "uniqueItems": {
+            "default": false,
+            "type": "boolean"
+        }
+    },
+    "type": "object"
+}

lib/spack/external/jsonschema/tests/compat.py

@@ -0,0 +1,15 @@
+import sys
+
+
+if sys.version_info[:2] < (2, 7):  # pragma: no cover
+    import unittest2 as unittest
+else:
+    import unittest
+
+try:
+    from unittest import mock
+except ImportError:
+    import mock
+
+
+# flake8: noqa

lib/spack/external/jsonschema/tests/test_cli.py

@@ -0,0 +1,110 @@
+from jsonschema import Draft4Validator, ValidationError, cli
+from jsonschema.compat import StringIO
+from jsonschema.tests.compat import mock, unittest
+
+
+def fake_validator(*errors):
+    errors = list(reversed(errors))
+
+    class FakeValidator(object):
+        def __init__(self, *args, **kwargs):
+            pass
+
+        def iter_errors(self, instance):
+            if errors:
+                return errors.pop()
+            return []
+    return FakeValidator
+
+
+class TestParser(unittest.TestCase):
+    FakeValidator = fake_validator()
+
+    def setUp(self):
+        mock_open = mock.mock_open()
+        patch_open = mock.patch.object(cli, "open", mock_open, create=True)
+        patch_open.start()
+        self.addCleanup(patch_open.stop)
+
+        mock_json_load = mock.Mock()
+        mock_json_load.return_value = {}
+        patch_json_load = mock.patch("json.load")
+        patch_json_load.start()
+        self.addCleanup(patch_json_load.stop)
+
+    def test_find_validator_by_fully_qualified_object_name(self):
+        arguments = cli.parse_args(
+            [
+                "--validator",
+                "jsonschema.tests.test_cli.TestParser.FakeValidator",
+                "--instance", "foo.json",
+                "schema.json",
+            ]
+        )
+        self.assertIs(arguments["validator"], self.FakeValidator)
+
+    def test_find_validator_in_jsonschema(self):
+        arguments = cli.parse_args(
+            [
+                "--validator", "Draft4Validator",
+                "--instance", "foo.json",
+                "schema.json",
+            ]
+        )
+        self.assertIs(arguments["validator"], Draft4Validator)
+
+
+class TestCLI(unittest.TestCase):
+    def test_successful_validation(self):
+        stdout, stderr = StringIO(), StringIO()
+        exit_code = cli.run(
+            {
+                "validator": fake_validator(),
+                "schema": {},
+                "instances": [1],
+                "error_format": "{error.message}",
+            },
+            stdout=stdout,
+            stderr=stderr,
+        )
+        self.assertFalse(stdout.getvalue())
+        self.assertFalse(stderr.getvalue())
+        self.assertEqual(exit_code, 0)
+
+    def test_unsuccessful_validation(self):
+        error = ValidationError("I am an error!", instance=1)
+        stdout, stderr = StringIO(), StringIO()
+        exit_code = cli.run(
+            {
+                "validator": fake_validator([error]),
+                "schema": {},
+                "instances": [1],
+                "error_format": "{error.instance} - {error.message}",
+            },
+            stdout=stdout,
+            stderr=stderr,
+        )
+        self.assertFalse(stdout.getvalue())
+        self.assertEqual(stderr.getvalue(), "1 - I am an error!")
+        self.assertEqual(exit_code, 1)
+
+    def test_unsuccessful_validation_multiple_instances(self):
+        first_errors = [
+            ValidationError("9", instance=1),
+            ValidationError("8", instance=1),
+        ]
+        second_errors = [ValidationError("7", instance=2)]
+        stdout, stderr = StringIO(), StringIO()
+        exit_code = cli.run(
+            {
+                "validator": fake_validator(first_errors, second_errors),
+                "schema": {},
+                "instances": [1, 2],
+                "error_format": "{error.instance} - {error.message}\t",
+            },
+            stdout=stdout,
+            stderr=stderr,
+        )
+        self.assertFalse(stdout.getvalue())
+        self.assertEqual(stderr.getvalue(), "1 - 9\t1 - 8\t2 - 7\t")
+        self.assertEqual(exit_code, 1)