SPACK-87: enable disabled git fetch tests.

- remove spurious mutually exclusive group from subparser.

README.md

@@ -32,20 +32,53 @@ Documentation
 [Full documentation](http://scalability-llnl.github.io/spack)
 for Spack is also available.
 
+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 currently using LLNL's old-fashioned
+mailing list software, so you'll need to click the links below and
+send the resulting email to subscribe or unsubscribe:
+
+  * **[Subscribe](mailto:majordomo@lists.llnl.gov?subject=subscribe&body=subscribe%20spack)**
+  * **[Unsubscribe](mailto:majordomo@lists.llnl.gov?subject=unsubscribe&body=unsubscribe%20spack)**
+
+### Contributions
+
+At the moment, contributing to Spack is relatively simple.  Just send us
+a [pull request](https://help.github.com/articles/using-pull-requests/).
+When you send your request, make ``develop`` the destination branch.
+
+Spack is using a rough approximation of the [Git
+Flow](http://nvie.com/posts/a-successful-git-branching-model/)
+branching model.  The ``develop`` branch contains the latest
+contributions, and ``master`` is always tagged and points to the
+latest stable release.
+
+
 Authors
 ----------------
 Spack was written by Todd Gamblin, tgamblin@llnl.gov.
 
-Significant contributions were also made by the following awesome
-people:
+Significant contributions were also made by:
 
   * David Beckingsale
   * David Boehme
+  * Alfredo Gimenez
   * Luc Jaulmes
   * Matt Legendre
   * Greg Lee
   * Adam Moody
+  * Saravan Pantham
+  * Joachim Protze
   * Bob Robey
+  * Justin Too
 
 Release
 ----------------

bin/spack

@@ -25,7 +25,8 @@
 ##############################################################################
 import sys
 if not sys.version_info[:2] >= (2,6):
-    sys.exit("Spack requires Python 2.6.  Version was %s." % sys.version_info)
+    v_info = sys.version_info[:3]
+    sys.exit("Spack requires Python 2.6 or higher.  This is Python %d.%d.%d." % v_info)
 
 import os
 
@@ -48,23 +49,39 @@ 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
 
 # Command parsing
 parser = argparse.ArgumentParser(
-    description='Spack: the Supercomputing PACKage Manager.')
+    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('-k', '--insecure', action='store_true',
+                    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)
-parser.add_argument('-v', '--verbose', action='store_true', dest='verbose',
-                    help="Print additional output during builds")
-parser.add_argument('-d', '--debug', action='store_true', dest='debug',
-                    help="Write out debug logs during compile")
-parser.add_argument('-k', '--insecure', action='store_true', dest='insecure',
-                    help="Do not check ssl certificates when downloading archives.")
-parser.add_argument('-m', '--mock', action='store_true', dest='mock',
-                    help="Use mock packages instead of real ones.")
 
 # each command module implements a parser() function, to which we pass its
 # subparser for setup.
@@ -84,33 +101,49 @@ if len(sys.argv) == 1:
 # actually parse the args.
 args = parser.parse_args()
 
-# Set up environment based on args.
-tty.set_verbose(args.verbose)
-tty.set_debug(args.debug)
-spack.debug = args.debug
+def main():
+    # Set up environment based on args.
+    tty.set_verbose(args.verbose)
+    tty.set_debug(args.debug)
+    spack.debug = args.debug
 
-spack.spack_working_dir = working_dir
-if args.mock:
-    from spack.packages import PackageDB
-    spack.db = PackageDB(spack.mock_packages_path)
+    spack.spack_working_dir = working_dir
+    if args.mock:
+        from spack.packages import PackageDB
+        spack.db = PackageDB(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.")
-    spack.curl.add_default_arg('-k')
+    # 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.")
+        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:
-    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)
+    # 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 KeyboardInterrupt:
+        sys.stderr.write('\n')
+        tty.die("Keyboard interrupt.")
+
+    # Allow commands to return values if they want to exit with some ohter code.
+    if return_val is None:
+        sys.exit(0)
+    elif isinstance(return_val, int):
+        sys.exit(return_val)
     else:
-        tty.die(e.message)
+        tty.die("Bad return value from command %s: %s" % (args.command, return_val))
 
-except KeyboardInterrupt:
-    tty.die("Keyboard interrupt.")
+if args.profile:
+    import cProfile
+    cProfile.run('main()', sort='tottime')
+else:
+    main()

lib/spack/docs/.gitignore

@@ -1,3 +1,4 @@
 package_list.rst
+command_index.rst
 spack*.rst
 _build

lib/spack/docs/Makefile

@@ -25,7 +25,19 @@ all: html
 # This autogenerates a package list.
 #
 package_list:
-	spack info -r > package_list.rst
+	spack package-list > package_list.rst
+
+#
+# Generate a command index
+#
+command_index:
+	cp command_index.in command_index.rst
+	echo >> command_index.rst
+	grep -ho '.. _spack-.*:' *rst \
+	| perl -pe 's/.. _([^:]*):/   * :ref:`\1`/' \
+	| sort >> command_index.rst
+
+custom_targets: package_list command_index
 
 #
 # This creates a git repository and commits generated html docs.
@@ -77,10 +89,10 @@ help:
 	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
 
 clean:
-	-rm -f package_list.rst
+	-rm -f package_list.rst command_index.rst
 	-rm -rf $(BUILDDIR)/* $(APIDOC_FILES)
 
-html: apidoc package_list
+html: apidoc custom_targets
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."

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 +1,36 @@
 <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 %}
+    {%- if last_updated %}
+      {% 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 @@
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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/basic_usage.rst

@@ -3,19 +3,18 @@
 Basic usage
 =====================
 
-Spack is implemented as a single command (``spack``) with many
-*subcommands*, much like ``git``, ``svn``, ``yum``, or ``apt-get``.
-Only a small subset of commands are needed for typical usage.
-
-This section covers a small set of subcommands that should cover most
-general use cases for Spack.
+The ``spack`` command has many *subcommands*.  You'll only need a
+small subset of them for typical usage.
 
 
 Listing available packages
 ------------------------------
 
-The first thing you will likely want to do with spack is find out what
-software is available to install.  There are a few relevant commands.
+To install software with Spack, you need to know what software is
+available.  You can see a list of available package names at the
+:ref:`package-list` webpage, or using the ``spack list`` command.
+
+.. _spack-list:
 
 ``spack list``
 ~~~~~~~~~~~~~~~~
@@ -26,45 +25,293 @@ Spack can install:
 .. command-output:: spack list
 
 The packages are listed by name in alphabetical order.  You can also
-do wildcard searches using ``*``:
+do wildcats searches using ``*``:
 
 .. command-output:: spack list m*
 
 .. command-output:: spack list *util*
 
+.. _spack-info:
 
 ``spack info``
 ~~~~~~~~~~~~~~~~
 
-To get information on a particular package from the full list, run
-``spack info <package name>``.  For example, for ``mpich`` the output
-looks like this:
+To get more information on a particular package from `spack list`, use
+`spack info`.  Just supply the name of a package:
 
 .. command-output:: spack info mpich
 
-This includes basic information about the package: where to download
-it, its dependencies, virtual packages it provides (e.g. an MPI
-implementation will provide the MPI interface), and a text
-description, if one is available.  :ref:`Dependencies
-<sec-specs>` and :ref:`virtual dependencies
+Most of the information is self-explanatory.  The *safe versions* are
+versions that Spack knows the checksum for, and it will use the
+checksum to verify that these versions download without errors or
+viruses.
+
+:ref:`Dependencies <sec-specs>` and :ref:`virtual dependencies
 <sec-virtual-dependencies>` are described in more detail later.
 
+.. _spack-versions:
+
 ``spack versions``
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
-To see available versions of a package, run ``spack versions``, for
-example:
+To see *more* available versions of a package, run ``spack versions``.
+For example:
 
 .. command-output:: spack versions libelf
 
-Since it has to manage many different software packages, Spack doesn't
-place many restrictions on what a package version has to look like.
-Packages like ``mpich`` use traditional version numbers like
-``3.0.4``. Other packages, like ``libdwarf`` use date-stamp versions
-like ``20130729``.  Versions can contain numbers, letters, dashes,
-underscores, and periods.
+There are two sections in the output.  *Safe versions* are versions
+for which Spack has a checksum on file.  It can verify that these
+versions are downloaded correctly.
 
-Compiler Configuration
+In many cases, Spack can also show you what versions are available out
+on the web---these are *remote versions*.  Spack gets this information
+by scraping it directly from package web pages.  Depending on the
+package and how its releases are organized, Spack may or may not be
+able to find remote versions.
+
+
+Installing and uninstalling
+------------------------------
+
+.. _spack-install:
+
+``spack install``
+~~~~~~~~~~~~~~~~~~~~~
+
+``spack install`` will install any package shown by ``spack list``.
+For example, To install the latest version of the ``mpileaks``
+package, you might type this:
+
+.. code-block:: sh
+
+   $ spack install mpileaks
+
+If `mpileaks` depends on other packages, Spack will install the
+dependencies first.  It then fetches the ``mpileaks`` tarball, expands
+it, verifies that it was downloaded without errors, builds it, and
+installs it in its own directory under ``$SPACK_ROOT/opt``. You'll see
+a number of messages from spack, a lot of build output, and a message
+that the packages is installed:
+
+.. code-block:: sh
+
+   $ spack install mpileaks
+   ==> Installing mpileaks
+   ==> mpich is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/mpich@3.0.4.
+   ==> callpath is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/callpath@1.0.2-5dce4318.
+   ==> adept-utils is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/adept-utils@1.0-5adef8da.
+   ==> Trying to fetch from https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
+   ######################################################################## 100.0%
+   ==> Staging archive: /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7=chaos_5_x86_64_ib-59f6ad23/mpileaks-1.0.tar.gz
+   ==> Created stage in /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7=chaos_5_x86_64_ib-59f6ad23.
+   ==> No patches needed for mpileaks.
+   ==> Building mpileaks.
+
+   ... build output ...
+
+   ==> Successfully installed mpileaks.
+     Fetch: 2.16s.  Build: 9.82s.  Total: 11.98s.
+   [+] /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/mpileaks@1.0-59f6ad23
+
+The last line, with the ``[+]``, indicates where the package is
+installed.
+
+Building a specific version
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Spack can also build *specific versions* of a package.  To do this,
+just add ``@`` after the package name, followed by a version:
+
+.. code-block:: sh
+
+   $ spack install mpich@3.0.4
+
+Any number of versions of the same package can be installed at once
+without interfering with each other.  This is good for multi-user
+sites, as installing a version that one user needs will not disrupt
+existing installations for other users.
+
+In addition to different versions, Spack can customize the compiler,
+compile-time options (variants), and platform (for cross compiles) of
+an installation.  Spack is unique in that it can also configure the
+*dependencies* a package is built with.  For example, two
+configurations of the same version of a package, one built with boost
+1.39.0, and the other version built with version 1.43.0, can coexist.
+
+This can all be done on the command line using the *spec* syntax.
+Spack calls the descriptor used to refer to a particular package
+configuration a **spec**.  In the commands above, ``mpileaks`` and
+``mpileaks@3.0.4``.  We'll talk more about how you can use them to
+customize an installation in :ref:`sec-specs`.
+
+.. _spack-uninstall:
+
+``spack uninstall``
+~~~~~~~~~~~~~~~~~~~~~
+
+To uninstall a package, type ``spack uninstall <package>``.  This will
+completely remove the directory in which the package was installed.
+
+.. code-block:: sh
+
+   spack uninstall mpich
+
+If there are still installed packages that depend on the package to be
+uninstalled, spack will refuse to uninstall it. You can override this
+behavior with ``spack uninstall -f <package>``, but you risk breaking
+other installed packages. In general, it is safer to remove dependent
+packages *before* removing their dependencies.
+
+A line like ``spack uninstall mpich`` may be ambiguous, if multiple
+``mpich`` configurations are installed.  For example, if both
+``mpich@3.0.2`` and ``mpich@3.1`` are installed, ``mpich`` could refer
+to either one. Because it cannot determine which one to uninstall,
+Spack will ask you to provide a version number to remove the
+ambiguity.  As an example, ``spack uninstall mpich@3.1`` is
+unambiguous in this scenario.
+
+
+Seeing installed packages
+-----------------------------------
+
+We know that ``spack list`` shows you the names of available packages,
+but how do you figure out which are installed?
+
+.. _spack-find:
+
+``spack find``
+~~~~~~~~~~~~~~~~~~~~~~
+
+``spack find`` shows the *specs* of installed packages.  A spec is
+like a name, but it has a version, compiler, architecture, and build
+options associated with it.  In spack, you can have many installations
+of the same package with different specs.
+
+Running ``spack find`` with no arguments lists installed packages:
+
+.. code-block:: sh
+
+   $ spack find
+   ==> 74 installed packages.
+   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+   ImageMagick@6.8.9-10  libdwarf@20130729  py-dateutil@2.4.0
+   adept-utils@1.0       libdwarf@20130729  py-ipython@2.3.1
+   atk@2.14.0            libelf@0.8.12      py-matplotlib@1.4.2
+   boost@1.55.0          libelf@0.8.13      py-nose@1.3.4
+   bzip2@1.0.6           libffi@3.1         py-numpy@1.9.1
+   cairo@1.14.0          libmng@2.0.2       py-pygments@2.0.1
+   callpath@1.0.2        libpng@1.6.16      py-pyparsing@2.0.3
+   cmake@3.0.2           libtiff@4.0.3      py-pyside@1.2.2
+   dbus@1.8.6            libtool@2.4.2      py-pytz@2014.10
+   dbus@1.9.0            libxcb@1.11        py-setuptools@11.3.1
+   dyninst@8.1.2         libxml2@2.9.2      py-six@1.9.0
+   fontconfig@2.11.1     libxml2@2.9.2      python@2.7.8
+   freetype@2.5.3        llvm@3.0           qhull@1.0
+   gdk-pixbuf@2.31.2     memaxes@0.5        qt@4.8.6
+   glib@2.42.1           mesa@8.0.5         qt@5.4.0
+   graphlib@2.0.0        mpich@3.0.4        readline@6.3
+   gtkplus@2.24.25       mpileaks@1.0       sqlite@3.8.5
+   harfbuzz@0.9.37       mrnet@4.1.0        stat@2.1.0
+   hdf5@1.8.13           ncurses@5.9        tcl@8.6.3
+   icu@54.1              netcdf@4.3.3       tk@src
+   jpeg@9a               openssl@1.0.1h     vtk@6.1.0
+   launchmon@1.0.1       pango@1.36.8       xcb-proto@1.11
+   lcms@2.6              pixman@0.32.6      xz@5.2.0
+   libdrm@2.4.33         py-dateutil@2.4.0  zlib@1.2.8
+
+   -- chaos_5_x86_64_ib / gcc@4.9.2 --------------------------------
+   libelf@0.8.10  mpich@3.0.4
+
+Packages are divided into groups according to their architecture and
+compiler.  Within each group, Spack tries to keep the view simple, and
+only shows the version of installed packages.
+
+In some cases, there may be different configurations of the *same*
+version of a package installed.  For example, there are two
+installations of of ``libdwarf@20130729`` above.  We can look at them
+in more detail using ``spack find -d``, and by asking only to show
+``libdwarf`` packages:
+
+.. code-block:: sh
+
+   $ spack find --deps libdwarf
+   ==> 2 installed packages.
+   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+       libdwarf@20130729-d9b90962
+           ^libelf@0.8.12
+       libdwarf@20130729-b52fac98
+           ^libelf@0.8.13
+
+Now we see that the two instances of ``libdwarf`` depend on
+*different* versions of ``libelf``: 0.8.12 and 0.8.13.  This view can
+become complicated for packages with many dependencies.  If you just
+want to know whether two packages' dependencies differ, you can use
+``spack find -l``:
+
+.. code-block:: sh
+
+   $ spack find -l libdwarf
+   ==> 2 installed packages.
+   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+   libdwarf@20130729-d9b90962  libdwarf@20130729-b52fac98
+
+Now the ``libwarf`` installs have hashes after their names.  These are
+hashes over all of the dependencies of each package.  If the hashes
+are the same, then the packages have the same dependency configuration.
+
+If you want to know the path where each package is installed, you can
+use ``spack find -p``:
+
+.. code-block:: sh
+
+   $ spack find -p
+   ==> 74 installed packages.
+   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+       ImageMagick@6.8.9-10  /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/ImageMagick@6.8.9-10-4df950dd
+       adept-utils@1.0       /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/adept-utils@1.0-5adef8da
+       atk@2.14.0            /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/atk@2.14.0-3d09ac09
+       boost@1.55.0          /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/boost@1.55.0
+       bzip2@1.0.6           /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/bzip2@1.0.6
+       cairo@1.14.0          /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/cairo@1.14.0-fcc2ab44
+       callpath@1.0.2        /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/callpath@1.0.2-5dce4318
+   ...
+
+And, finally, you can restrict your search to a particular package
+by supplying its name:
+
+.. code-block:: sh
+
+   $ spack find -p libelf
+   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+       libelf@0.8.11  /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.11
+       libelf@0.8.12  /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.12
+       libelf@0.8.13  /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.13
+
+``spack find`` actually does a lot more than this.  You can use
+*specs* to query for specific configurations and builds of each
+package. If you want to find only libelf versions greater than version
+0.8.12, you could say:
+
+.. code-block:: sh
+
+   $ spack find libelf@0.8.12:
+   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+       libelf@0.8.12  libelf@0.8.13
+
+Finding just the versions of libdwarf built with a particular version
+of libelf would look like this:
+
+.. code-block:: sh
+
+   $ spack find -l libdwarf ^libelf@0.8.12
+   ==> 1 installed packages.
+   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+   libdwarf@20130729-d9b90962
+
+The full spec syntax is discussed in detail in :ref:`sec-specs`.
+
+
+Compiler configuration
 -----------------------------------
 
 Spack has the ability to build packages with multiple compilers and
@@ -72,6 +319,8 @@ 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``
 ~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -98,6 +347,8 @@ compilers`` or ``spack compiler list``::
 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``
 ~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -110,15 +361,19 @@ where the compiler is installed.  For example::
         intel@13.0.079
 
 Or you can run ``spack compiler add`` with no arguments to force
-autodetection.  This is useful if you do not know where compilers
-live, but new compilers have been added to your ``PATH``.  For
-example, using dotkit, you might do this::
+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::
 
-    $ use gcc-4.9.0
+    $ module load gcc-4.9.0
     $ spack compiler add
     ==> Added 1 new compiler to /Users/gamblin2/.spackconfig
         gcc@4.9.0
 
+This loads the environment module for gcc-4.9.0 to get it into the
+``PATH``, and then it adds the compiler to Spack.
+
+.. _spack-compiler-info:
 
 ``spack compiler info``
 ~~~~~~~~~~~~~~~~~~~~~~~
@@ -126,20 +381,23 @@ example, using dotkit, you might do this::
 If you want to see specifics on a particular compiler, you can run
 ``spack compiler info`` on it::
 
-    $ spack compiler info intel@12.1.3
-    intel@12.1.3:
-    cc  = /usr/local/bin/icc-12.1.293
-    cxx = /usr/local/bin/icpc-12.1.293
-    f77 = /usr/local/bin/ifort-12.1.293
-    fc = /usr/local/bin/ifort-12.1.293
+   $ 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 configuration
-~~~~~~~~~~~~~~~~~~~~~~~
+Manual compiler configuration
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-If autodetection fails, you can manually conigure a compiler by
+If auto-detection fails, you can manually configure a compiler by
 editing your ``~/.spackconfig`` file.  You can do this by running
 ``spack config edit``, which will open the file in your ``$EDITOR``.
 
@@ -153,8 +411,8 @@ Each compiler configuration in the file looks like this::
         fc = /usr/local/bin/ifort-15.0.024-beta
     ...
 
-For compilers, like ``clang``, that do not support Fortran, you can simply
-put ``None`` for ``f77`` and ``fc``::
+For compilers, like ``clang``, that do not support Fortran, put
+``None`` for ``f77`` and ``fc``::
 
     [compiler "clang@3.3svn"]
         cc = /usr/bin/clang
@@ -163,180 +421,18 @@ put ``None`` for ``f77`` and ``fc``::
         fc = None
 
 Once you save the file, the configured compilers will show up in the
-list displayed when you run ``spack compilers``.
-
-
-Seeing installed packages -----------------------------------
-
-``spack find``
-~~~~~~~~~~~~~~~~~~~~~~
-
-The second thing you're likely to want to do with Spack, and the first
-thing users of your system will likely want to do, is to find what
-software is already installed and ready to use.  You can do that with
-``spack find``.
-
-Running ``spack find`` with no arguments will list all the installed
-packages:
-
-.. code-block:: sh
-
-   $ spack find
-   == chaos_5_x86_64_ib ===========================================
-   -- gcc@4.4.7 ---------------------------------------------------
-       libdwarf@20130207-d9b909
-       libdwarf@20130729-d9b909
-       libdwarf@20130729-b52fac
-       libelf@0.8.11
-       libelf@0.8.12
-       libelf@0.8.13
-
-Packages are grouped by architecture, then by the compiler used to
-build them, and then by their versions and options.  If a package has
-dependencies, there will also be a hash at the end of the name
-indicating the dependency configuration.  Packages with the same hash
-have the same dependency configuration.  If you want ALL information
-about dependencies, as well, then you can supply ``-l`` or ``--long``:
-
-.. code-block:: sh
-
-   $ spack find -l
-   == chaos_5_x86_64_ib ===========================================
-   -- gcc@4.4.7 ---------------------------------------------------
-       libdwarf@20130207
-           ^libelf@0.8.12
-       libdwarf@20130729
-           ^libelf@0.8.12
-       libdwarf@20130729
-           ^libelf@0.8.13
-       libelf@0.8.11
-       libelf@0.8.12
-       libelf@0.8.13
-
-Now you can see which versions of ``libelf`` each version of
-``libdwarf`` was built with.
-
-If you want to know the path where each of these packages is
-installed, do ``spack find -p`` or ``--path``:
-
-.. code-block:: sh
-
-   $ spack find -p
-   == chaos_5_x86_64_ib ===========================================
-   -- gcc@4.4.7 ---------------------------------------------------
-       libdwarf@20130207-d9b909  /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libdwarf@20130207-d9b909
-       libdwarf@20130729-d9b909  /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libdwarf@20130729-d9b909
-       libdwarf@20130729-b52fac  /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libdwarf@20130729-b52fac
-       libelf@0.8.11             /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.11
-       libelf@0.8.12             /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.12
-       libelf@0.8.13             /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.13
-
-
-And, finally, you can restrict your search to a particular package
-by supplying its name:
-
-.. code-block:: sh
-
-   $ spack find -p libelf
-   == chaos_5_x86_64_ib ===========================================
-   -- gcc@4.4.7 ---------------------------------------------------
-       libelf@0.8.11  /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.11
-       libelf@0.8.12  /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.12
-       libelf@0.8.13  /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.13
-
-
-``spack find`` actually does a lot more than this.  You can use
-*specs* to query for specific configurations and builds of each
-package.  The full spec syntax is discussed in detail in
-:ref:`sec-specs`.
-
-
-
-Installing and uninstalling
-------------------------------
-
-``spack install``
-~~~~~~~~~~~~~~~~~~~~~
-
-``spack install`` will install any package that appears in the output
-of ``spack list``.  To install the latest version of a pacakge and all
-of its dependencies, simply run ``spack install <package>``:
-
-.. code-block:: sh
-
-   spack install mpileaks
-
-Spack will fetch the tarball for ``mpileaks``, expand it, verify that
-it was downloaded without errors, build it, and install it in its own
-directory under ``$SPACK_HOME/opt``.  If the requested package depends
-on other packages in order to build, Spack fetches them as well, and
-installs them before it installs the requested package. Like the main
-package, each dependency is also installed in its own directory.
-
-Spack can also build *specific* configurations of a package.  For
-example, to install something with a specific version, add ``@`` after
-the package name, followed by a version string:
-
-.. code-block:: sh
-
-   spack install mpich@3.0.4
-
-Any number of configurations of the same package can be installed at
-once without interfering with each other.  This is good for multi-user
-sites, as installing a version that one user needs will not disrupt
-existing installations for other users.
-
-In addition to version configuraitons, Spack can customize the
-compiler, compile-time options (variants), and platform (for cross
-compiles) of an installation.  Spack is unique in that it can also
-configure the *dependencies* a package is built with.  For example,
-two configurations of the same version of a package, one built with
-boost 1.39.0, and the other version built with version 1.43.0, can
-coexist.
-
-This can all be done on the command line using special syntax.  Spack
-calls the descriptor used to refer to a particular package
-configuration a **spec**.  In the command lines above, both
-``mpileaks`` and ``mpileaks@3.0.4`` are specs.  To customize
-additional properties, simply add more attributes to the spec.  Specs
-and their syntax are covered in more detail in :ref:`sec-specs`.
-
-
-``spack uninstall``
-~~~~~~~~~~~~~~~~~~~~~
-
-To uninstall a package, type ``spack uninstall <package>``.  This will
-completely remove the directory in which the package was installed.
-
-.. code-block:: sh
-
-   spack uninstall mpich
-
-If there are still installed packages that depend on the package to be
-uninstalled, spack will refuse to uninstall.  If you know what you're
-doing, you can override this with ``spack uninstall -f <package>``.
-However, running this risks breaking other installed packages. In
-general, it is safer to remove dependent packages *before* removing
-their dependencies.
-
-A line like ``spack uninstall mpich`` may be ambiguous, if multiple
-``mpich`` configurations are installed.  For example, if both
-``mpich@3.0.2`` and ``mpich@3.1`` are installed, it could refer to
-either one, and Spack cannot determine which one to uninstall.  Spack
-will ask you to provide a version number to remove the ambiguity.  For
-example, ``spack uninstall mpich@3.1`` is unambiguous in the above
-scenario.
+list displayed by ``spack compilers``.
 
 
 .. _sec-specs:
 
-Specs & Dependencies
+Specs & dependencies
 -------------------------
 
-We now know that ``spack install`` and ``spack uninstall`` both take a
-package name with an optional version specifier.  In Spack, that
-descriptor is called a *spec*.  Spack uses specs to refer to a
-particular build configuration (or configurations) of a package.
+We know that ``spack install``, ``spack uninstall``, and other
+commands take a package name with an optional version specifier.  In
+Spack, that descriptor is called a *spec*.  Spack uses specs to refer
+to a particular build configuration (or configurations) of a package.
 Specs are more than a package name and a version; you can use them to
 specify the compiler, compiler version, architecture, compile options,
 and dependency options for a build.  In this section, we'll go over
@@ -499,6 +595,11 @@ based on site policies.
 Variants
 ~~~~~~~~~~~~~~~~~~~~~~~
 
+.. Note::
+
+   Variants are not yet supported, but will be in the next Spack
+   release (0.9), due in Q2 2015.
+
 Variants are named options associated with a particular package, and
 they can be turned on or off.  For example, above, supplying
 ``+debug`` causes ``mpileaks`` to be built with debug flags.  The
@@ -544,6 +645,11 @@ the command line is provided for convenience and legibility.
 Architecture specifier
 ~~~~~~~~~~~~~~~~~~~~~~~
 
+.. Note::
+
+   Architecture specifiers are part of specs but are not yet
+   functional. They will be in Spack version 1.0, due in Q3 2015.
+
 The architecture specifier starts with a ``=`` and also comes after
 some package name within a spec.  It allows a user to specify a
 particular architecture for the package to be built.  This is mostly
@@ -627,6 +733,8 @@ any MPI implementation will do.  If another package depends on
 error.  Likewise, if you try to plug in some package that doesn't
 provide MPI, Spack will raise an error.
 
+.. _spack-providers:
+
 ``spack providers``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -646,7 +754,7 @@ versions are now filtered out.
 
 .. _shell-support:
 
-Environment Modules
+Environment modules
 -------------------------------
 
 .. note::
@@ -678,10 +786,6 @@ For ``csh`` and ``tcsh`` run:
 You can put the above code in your ``.bashrc`` or ``.cshrc``, and
 Spack's shell support will be available on the command line.
 
-
--------------------------------
-
-
 When you install a package with Spack, it automatically generates an
 environment module that lets you add the package to your environment.
 
@@ -698,6 +802,7 @@ The directories are automatically added to your ``MODULEPATH`` and
 ``DK_NODE`` environment variables when you enable Spack's `shell
 support <shell-support_>`_.
 
+
 Using Modules & Dotkits
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -710,7 +815,7 @@ of installed packages.
 
      $ module avail
 
-     ------- /g/g21/gamblin2/src/spack/share/spack/modules/chaos_5_x86_64_ib --------
+     ------- /home/gamblin2/spack/share/spack/modules/chaos_5_x86_64_ib --------
      adept-utils@1.0%gcc@4.4.7-5adef8da   libelf@0.8.13%gcc@4.4.7
      automaded@1.0%gcc@4.4.7-d9691bb0     libelf@0.8.13%intel@15.0.0
      boost@1.55.0%gcc@4.4.7               mpc@1.0.2%gcc@4.4.7-559607f5
@@ -845,6 +950,8 @@ if newer, fancier module support is added to Spack at some later date,
 you may want to regenerate all the modules to take advantage of these
 new features.
 
+.. _spack-module:
+
 ``spack module refresh``
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -858,9 +965,226 @@ regenerate all module and dotkit files from scratch:
    ==> Regenerating tcl module files.
    ==> Regenerating dotkit module files.
 
+
+.. _extensions:
+
+Extensions & Python support
+------------------------------------
+
+Spack's installation model assumes that each package will live in its
+own install prefix.  However, certain packages are typically installed
+*within* the directory hierarchy of other packages.  For example,
+modules in interpreted languages like `Python
+<https://www.python.org>`_ are typically installed in the
+``$prefix/lib/python-2.7/site-packages`` directory.
+
+Spack has support for this type of installation as well.  In Spack,
+a package that can live inside the prefix of another package is called
+an *extension*.  Suppose you have Python installed like so:
+
+.. code-block:: sh
+
+   $ spack find python
+   ==> 1 installed packages.
+   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+   python@2.7.8
+
+.. _spack-extensions:
+
+``spack extensions``
+~~~~~~~~~~~~~~~~~~~~~~~
+
+You can find extensions for your Python installation like this:
+
+.. code-block:: sh
+
+   $ spack extensions python
+   ==> python@2.7.8%gcc@4.4.7=chaos_5_x86_64_ib-703c7a96
+   ==> 36 extensions:
+   geos          py-ipython     py-pexpect    py-pyside            py-sip
+   py-basemap    py-libxml2     py-pil        py-pytz              py-six
+   py-biopython  py-mako        py-pmw        py-rpy2              py-sympy
+   py-cython     py-matplotlib  py-pychecker  py-scientificpython  py-virtualenv
+   py-dateutil   py-mpi4py      py-pygments   py-scikit-learn
+   py-epydoc     py-mx          py-pylint     py-scipy
+   py-gnuplot    py-nose        py-pyparsing  py-setuptools
+   py-h5py       py-numpy       py-pyqt       py-shiboken
+
+   ==> 12 installed:
+   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+   py-dateutil@2.4.0    py-nose@1.3.4       py-pyside@1.2.2
+   py-dateutil@2.4.0    py-numpy@1.9.1      py-pytz@2014.10
+   py-ipython@2.3.1     py-pygments@2.0.1   py-setuptools@11.3.1
+   py-matplotlib@1.4.2  py-pyparsing@2.0.3  py-six@1.9.0
+
+   ==> None activated.
+
+The extensions are a subset of what's returned by ``spack list``, and
+they are packages like any other.  They are installed into their own
+prefixes, and you can see this with ``spack find -p``:
+
+.. code-block:: sh
+
+   $ spack find -p py-numpy
+   ==> 1 installed packages.
+   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+       py-numpy@1.9.1  /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/py-numpy@1.9.1-66733244
+
+However, even though this package is installed, you cannot use it
+directly when you run ``python``:
+
+.. code-block:: sh
+
+   $ spack load python
+   $ python
+   Python 2.7.8 (default, Feb 17 2015, 01:35:25)
+   [GCC 4.4.7 20120313 (Red Hat 4.4.7-11)] on linux2
+   Type "help", "copyright", "credits" or "license" for more information.
+   >>> import numpy
+   Traceback (most recent call last):
+     File "<stdin>", line 1, in <module>
+   ImportError: No module named numpy
+   >>>
+
+Extensions & Environment Modules
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+There are two ways to get ``numpy`` working in Python.  The first is
+to use :ref:`shell-support`.  You can simply ``use`` or ``load`` the
+module for the extension, and it will be added to the ``PYTHONPATH``
+in your current shell.
+
+For tcl modules:
+
+.. code-block:: sh
+
+   $ spack load python
+   $ spack load py-numpy
+
+or, for dotkit:
+
+.. code-block:: sh
+
+   $ spack use python
+   $ spack use py-numpy
+
+Now ``import numpy`` will succeed for as long as you keep your current
+session open.
+
+
+Activating Extensions
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+It is often desirable to have certain packages *always* available as
+part of a Python installation.  Spack offers a more permanent solution
+for this case.  Instead of requiring users to load particular
+environment modules, you can *activate* the package within the Python
+installation:
+
+.. _spack-activate:
+
+``spack activate``
+^^^^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: sh
+
+   $ spack activate py-numpy
+   ==> Activated extension py-setuptools@11.3.1%gcc@4.4.7=chaos_5_x86_64_ib-3c74eb69 for python@2.7.8%gcc@4.4.7.
+   ==> Activated extension py-nose@1.3.4%gcc@4.4.7=chaos_5_x86_64_ib-5f70f816 for python@2.7.8%gcc@4.4.7.
+   ==> Activated extension py-numpy@1.9.1%gcc@4.4.7=chaos_5_x86_64_ib-66733244 for python@2.7.8%gcc@4.4.7.
+
+Several things have happened here.  The user requested that
+``py-numpy`` be activated in the ``python`` installation it was built
+with.  Spack knows that ``py-numpy`` depends on ``py-nose`` and
+``py-setuptools``, so it activated those packages first.  Finally,
+once all dependencies were activated in the ``python`` installation,
+``py-numpy`` was activated as well.
+
+If we run ``spack extensions`` again, we now see the three new
+packages listed as activated:
+
+.. code-block:: sh
+
+   $ spack extensions python
+   ==> python@2.7.8%gcc@4.4.7=chaos_5_x86_64_ib-703c7a96
+   ==> 36 extensions:
+   geos          py-ipython     py-pexpect    py-pyside            py-sip
+   py-basemap    py-libxml2     py-pil        py-pytz              py-six
+   py-biopython  py-mako        py-pmw        py-rpy2              py-sympy
+   py-cython     py-matplotlib  py-pychecker  py-scientificpython  py-virtualenv
+   py-dateutil   py-mpi4py      py-pygments   py-scikit-learn
+   py-epydoc     py-mx          py-pylint     py-scipy
+   py-gnuplot    py-nose        py-pyparsing  py-setuptools
+   py-h5py       py-numpy       py-pyqt       py-shiboken
+
+   ==> 12 installed:
+   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+   py-dateutil@2.4.0    py-nose@1.3.4       py-pyside@1.2.2
+   py-dateutil@2.4.0    py-numpy@1.9.1      py-pytz@2014.10
+   py-ipython@2.3.1     py-pygments@2.0.1   py-setuptools@11.3.1
+   py-matplotlib@1.4.2  py-pyparsing@2.0.3  py-six@1.9.0
+
+   ==> 3 currently activated:
+   -- chaos_5_x86_64_ib / gcc@4.4.7 --------------------------------
+   py-nose@1.3.4  py-numpy@1.9.1  py-setuptools@11.3.1
+
+
+Now, when a user runs python, ``numpy`` will be available for import
+*without* the user having to explicitly loaded.  ``python@2.7.8`` now
+acts like a system Python installation with ``numpy`` installed inside
+of it.
+
+Spack accomplishes this by symbolically linking the *entire* prefix of
+the ``py-numpy`` into the prefix of the ``python`` package.  To the
+python interpreter, it looks like ``numpy`` is installed in the
+``site-packages`` directory.
+
+The only limitation of activation is that you can only have a *single*
+version of an extension activated at a time.  This is because multiple
+versions of the same extension would conflict if symbolically linked
+into the same prefix.  Users who want a different version of a package
+can still get it by using environment modules, but they will have to
+explicitly load their preferred version.
+
+``spack activate -f``
+^^^^^^^^^^^^^^^^^^^^^^^^^
+If, for some reason, you want to activate a package *without* its
+dependencies, you can use ``spack activate -f``:
+
+.. code-block:: sh
+
+   $ spack activate -f py-numpy
+   ==> Activated extension py-numpy@1.9.1%gcc@4.4.7=chaos_5_x86_64_ib-66733244 for python@2.7.8%gcc@4.4.7.
+
+.. _spack-deactivate:
+
+``spack deactivate``
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+We've seen how activating an extension can be used to set up a default
+version of a Python module.  Obviously, you may want to change that at
+some point.  ``spack deactivate`` is the command for this.  There are
+several variants:
+
+  * ``spack deactivate <extension>`` will deactivate a single
+    extension.  If another activated extension depends on this one,
+    Spack will warn you and exit with an error.
+  * ``spack deactivate -f <extension>`` deactivates an extension
+    regardless of packages that depend on it.
+  * ``spack deactivate -a <extension>`` deactivates an extension and
+    all of its dependencies.  Use ``-f`` to disregard dependents.
+  * ``spack deactivate -a <extendee>`` deactivates *all* activated
+    extensions of a package.  For example, to deactivate *all* python
+    extensions, use::
+
+       spack deactivate -a python
+
+
 Getting Help
 -----------------------
 
+.. _spack-help:
+
 ``spack help``
 ~~~~~~~~~~~~~~~~~~~~~~
 

lib/spack/docs/command_index.in

@@ -0,0 +1,10 @@
+.. _command_index:
+
+Command index
+=================
+
+This is an alphabetical list of commands with links to the places they
+appear in the documentation.
+
+.. hlist::
+   :columns: 3

lib/spack/docs/conf.py

@@ -35,7 +35,9 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys, os
+import sys
+import os
+import subprocess
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -43,14 +45,16 @@
 sys.path.insert(0, os.path.abspath('exts'))
 
 # Add the Spack bin directory to the path so that we can use its output in docs.
-os.environ['SPACK_ROOT'] = '../../..'
+spack_root = '../../..'
+os.environ['SPACK_ROOT'] = spack_root
 os.environ['PATH'] += os.pathsep + '$SPACK_ROOT/bin'
 
+spack_version =  subprocess.Popen(
+    ['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.
-os.environ['COLIFY_TTY'] = 'true'
-os.environ['COLUMNS']    = '80'
-os.environ['LINES']      = '25'
+os.environ['COLIFY_SIZE'] = '25x80'
 
 # Enable todo items
 todo_include_todos = True
@@ -83,7 +87,7 @@
 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'
@@ -97,9 +101,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.0'
+version = '.'.join(spack_version[:2])
 # The full version, including alpha/beta/rc tags.
-release = '1.0'
+release = '.'.join(spack_version[:2])
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -145,7 +149,7 @@
 # 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 = [('show_copyright', False)]
 
 # Add any paths that contain custom themes here, relative to this directory.
 html_theme_path = ["_themes"]

lib/spack/docs/developer_guide.rst

@@ -50,11 +50,11 @@ as a descriptor for one or more instances of that template.  Users
 express the configuration they want using a spec, and a package turns
 the spec into a complete build.
 
-The obvious difficulty with this design is that users underspecify
+The obvious difficulty with this design is that users under-specify
 what they want.  To build a software package, the package object needs
 a *complete* specification.  In Spack, if a spec describes only one
 instance of a package, then we say it is **concrete**.  If a spec
-could describes many instances, (i.e. it is underspecified in one way
+could describes many instances, (i.e. it is under-specified in one way
 or another), then we say it is **abstract**.
 
 Spack's job is to take an *abstract* spec from the user, find a
@@ -92,7 +92,7 @@ with a high level view of Spack's directory structure::
 Spack is designed so that it could live within a `standard UNIX
 directory hierarchy <http://linux.die.net/man/7/hier>`_, so ``lib``,
 ``var``, and ``opt`` all contain a ``spack`` subdirectory in case
-Spack is installed alongside other software.  Most of the insteresting
+Spack is installed alongside other software.  Most of the interesting
 parts of Spack live in ``lib/spack``.  Files under ``var`` are created
 as needed, so there is no ``var`` directory when you initially clone
 Spack from the repository.
@@ -123,13 +123,13 @@ Package-related modules
   Contains the :class:`Package <spack.package.Package>` class, which
   is the superclass for all packages in Spack.  Methods on ``Package``
   implement all phases of the :ref:`package lifecycle
-  <pacakge-lifecycle>` and manage the build process.
+  <package-lifecycle>` and manage the build process.
 
 :mod:`spack.packages`
   Contains all of the packages in Spack and methods for managing them.
   Functions like :func:`packages.get <spack.packages.get>` and
   :func:`class_name_for_package_name
-  <packages.class_name_for_package_name>` handle mapping packge module
+  <packages.class_name_for_package_name>` handle mapping package module
   names to class names and dynamically instantiating packages by name
   from module files.
 

lib/spack/docs/features.rst

@@ -1,4 +1,4 @@
-Feature Overview
+Feature overview
 ==================
 
 This is a high-level overview of features that make Spack different

lib/spack/docs/getting_started.rst

@@ -12,20 +12,30 @@ Getting spack is easy.  You can clone it from the `github repository
    $ git clone https://github.com/scalability-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 ``$SPACK_HOME/bin`` to your path and you're ready
-to go:
+full path to this directory is in the ``SPACK_ROOT`` environment
+variable.  Add ``$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://scalability-llnl.github.io/spack/basic_usage.html#environment-modules>`_:
 
+.. code-block:: sh
 
-Install
+   # 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``.
+
+Installation
 --------------------
 
 You don't need to install Spack; it's ready to run as soon as you
@@ -39,6 +49,7 @@ 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.

lib/spack/docs/index.rst

@@ -18,8 +18,8 @@ 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 writtin 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.
 
@@ -46,8 +46,10 @@ Table of Contents
    getting_started
    basic_usage
    packaging_guide
+   mirrors
    site_configuration
    developer_guide
+   command_index
    package_list
    API Docs <spack>
 

lib/spack/docs/mirrors.rst

@@ -0,0 +1,217 @@
+.. _mirrors:
+
+Mirrors
+============================
+
+Some sites may not have access to the internet for fetching packages.
+These sites will need a local repository of tarballs from which they
+can get their files.  Spack has support for this with *mirrors*.  A
+mirror is a URL that points to a directory, either on the local
+filesystem or on some server, containing tarballs for all of Spack's
+packages.
+
+Here's an example of a mirror's directory structure::
+
+    mirror/
+        cmake/
+            cmake-2.8.10.2.tar.gz
+        dyninst/
+            dyninst-8.1.1.tgz
+            dyninst-8.1.2.tgz
+        libdwarf/
+            libdwarf-20130126.tar.gz
+            libdwarf-20130207.tar.gz
+            libdwarf-20130729.tar.gz
+        libelf/
+            libelf-0.8.12.tar.gz
+            libelf-0.8.13.tar.gz
+        libunwind/
+            libunwind-1.1.tar.gz
+        mpich/
+            mpich-3.0.4.tar.gz
+        mvapich2/
+            mvapich2-1.9.tgz
+
+The structure is very simple.  There is a top-level directory.  The
+second level directories are named after packages, and the third level
+contains tarballs for each package, named after each package.
+
+.. note::
+
+   Archives are **not** named exactly 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
+   package's fetch URL contains.
+
+   In order to make mirror creation reasonably fast, we copy the
+   tarball in its original format to the mirror directory, but we do
+   not standardize on a particular compression algorithm, because this
+   would potentially require expanding and re-compressing each archive.
+
+.. _spack-mirror:
+
+``spack mirror``
+----------------------------
+
+Mirrors are managed with the ``spack mirror`` command.  The help for
+``spack mirror`` looks like this::
+
+    $ spack mirror -h
+    usage: spack mirror [-h] SUBCOMMAND ...
+
+    positional arguments:
+      SUBCOMMAND
+        create           Create a directory to be used as a spack mirror, and fill
+                         it with package archives.
+        add              Add a mirror to Spack.
+        remove           Remove a mirror by name.
+        list             Print out available mirrors to the console.
+
+    optional arguments:
+      -h, --help         show this help message and exit
+
+The ``create`` command actually builds a mirror by fetching all of its
+packages from the internet and checksumming them.
+
+The other three commands are for managing mirror configuration.  They
+control the URL(s) from which Spack downloads its packages.
+
+.. _spack-mirror-create:
+
+``spack mirror create``
+----------------------------
+
+You can create a mirror using the ``spack mirror create`` command, assuming
+you're on a machine where you can access the internet.
+
+The command will iterate through all of Spack's packages and download
+the safe ones into a directory structure like the one above.  Here is
+what it looks like:
+
+
+.. code-block:: bash
+
+   $ spack mirror create libelf libdwarf
+   ==> Created new mirror in spack-mirror-2014-06-24
+   ==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.13.tar.gz
+   ##########################################################                81.6%
+   ==> Checksum passed for libelf@0.8.13
+   ==> Added libelf@0.8.13
+   ==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.12.tar.gz
+   ######################################################################    98.6%
+   ==> Checksum passed for libelf@0.8.12
+   ==> Added libelf@0.8.12
+   ==> Trying to fetch from http://www.prevanders.net/libdwarf-20130207.tar.gz
+   ######################################################################    97.3%
+   ==> Checksum passed for libdwarf@20130207
+   ==> Added libdwarf@20130207
+   ==> Trying to fetch from http://www.prevanders.net/libdwarf-20130126.tar.gz
+   ########################################################                  78.9%
+   ==> Checksum passed for libdwarf@20130126
+   ==> Added libdwarf@20130126
+   ==> Trying to fetch from http://www.prevanders.net/libdwarf-20130729.tar.gz
+   #############################################################             84.7%
+   ==> Added libdwarf@20130729
+   ==> Added spack-mirror-2014-06-24/libdwarf/libdwarf-20130729.tar.gz to mirror
+   ==> Added python@2.7.8.
+   ==> Successfully updated mirror in spack-mirror-2015-02-24.
+     Archive stats:
+       0    already present
+       5    added
+       0    failed to fetch.
+
+Once this is done, you can tar up the ``spack-mirror-2014-06-24`` directory and
+copy it over to the machine you want it hosted on.
+
+Custom package sets
+~~~~~~~~~~~~~~~~~~~~~~~
+
+Normally, ``spack mirror create`` downloads all the archives it has
+checksums for.  If you want to only create a mirror for a subset of
+packages, you can do that by supplying a list of package specs on the
+command line after ``spack mirror create``.  For example, this
+command::
+
+    $ spack mirror create libelf@0.8.12: boost@1.44:
+
+Will create a mirror for libelf versions greater than or equal to
+0.8.12 and boost versions greater than or equal to 1.44.
+
+Mirror files
+~~~~~~~~~~~~~~~~~~~~~~~
+
+If you have a *very* large number of packages you want to mirror, you
+can supply a file with specs in it, one per line::
+
+   $ cat specs.txt
+   libdwarf
+   libelf@0.8.12:
+   boost@1.44:
+   boost@1.39.0
+   ...
+   $ spack mirror create -f specs.txt
+   ...
+
+This is useful if there is a specific suite of software managed by
+your site.
+
+.. _spack-mirror-add:
+
+``spack mirror add``
+----------------------------
+
+Once you have a mirror, you need to let spack know about it.  This is
+relatively simple.  First, figure out the URL for the mirror.  If it's
+a file, you can use a file URL like this one::
+
+    file:///Users/gamblin2/spack-mirror-2014-06-24
+
+That points to the directory on the local filesystem.  If it were on a
+web server, you could use a URL like this one:
+
+    https://example.com/some/web-hosted/directory/spack-mirror-2014-06-24
+
+Spack will use the URL as the root for all of the packages it fetches.
+You can tell your Spack installation to use that mirror like this:
+
+.. code-block:: bash
+
+   $ spack mirror add local_filesystem file:///Users/gamblin2/spack-mirror-2014-06-24
+
+Each mirror has a name so that you can refer to it again later.
+
+.. _spack-mirror-list:
+
+``spack mirror list``
+----------------------------
+
+If you want to see all the mirrors Spack knows about you can run ``spack mirror list``::
+
+   $ spack mirror list
+   local_filesystem    file:///Users/gamblin2/spack-mirror-2014-06-24
+
+.. _spack-mirror-remove:
+
+``spack mirror remove``
+----------------------------
+
+And, if you want to remove a mirror, just remove it by name::
+
+   $ spack mirror remove local_filesystem
+   $ spack mirror list
+   ==> No mirrors configured.
+
+Mirror precedence
+----------------------------
+
+Adding a mirror really just adds a section in ``~/.spackconfig``::
+
+   [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
+
+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.

lib/spack/docs/site_configuration.rst

@@ -1,208 +1,16 @@
 .. _site-configuration:
 
-Site-specific configuration
+Site configuration
 ===================================
 
-.. _mirrors:
-
-Mirrors
-----------------------------
-
-Some sites may not have access to the internet for fetching packages.
-These sites will need a local repository of tarballs from which they
-can get their files.  Spack has support for this with *mirrors*.  A
-mirror is a URL that points to a directory, either on the local
-filesystem or on some server, containing tarballs for all of Spack's
-packages.
-
-Here's an example of a mirror's directory structure::
-
-    mirror/
-        cmake/
-            cmake-2.8.10.2.tar.gz
-        dyninst/
-            DyninstAPI-8.1.1.tgz
-            DyninstAPI-8.1.2.tgz
-        libdwarf/
-            libdwarf-20130126.tar.gz
-            libdwarf-20130207.tar.gz
-            libdwarf-20130729.tar.gz
-        libelf/
-            libelf-0.8.12.tar.gz
-            libelf-0.8.13.tar.gz
-        libunwind/
-            libunwind-1.1.tar.gz
-        mpich/
-            mpich-3.0.4.tar.gz
-        mvapich2/
-        mvapich2-1.9.tgz
-
-The structure is very simple.  There is a top-level directory.  The
-second level directories are named after packages, and the third level
-contains tarballs for each package, named as they were in the
-package's fetch URL.
-
-``spack mirror``
-~~~~~~~~~~~~~~~~~~~~~~~
-
-Mirrors are managed with the ``spack mirror`` command.  The help for
-``spack mirror`` looks like this::
-
-    $ spack mirror -h
-    usage: spack mirror [-h] SUBCOMMAND ...
-
-    positional arguments:
-      SUBCOMMAND
-        create           Create a directory to be used as a spack mirror, and fill
-                         it with package archives.
-        add              Add a mirror to Spack.
-        remove           Remove a mirror by name.
-        list             Print out available mirrors to the console.
-
-    optional arguments:
-      -h, --help         show this help message and exit
-
-The ``create`` command actually builds a mirror by fetching all of its
-packages from the internet and checksumming them.
-
-The other three commands are for managing mirror configuration.  They
-control the URL(s) from which Spack downloads its packages.
-
-
-``spack mirror create``
-~~~~~~~~~~~~~~~~~~~~~~~
-
-You can create a mirror using the ``spack mirror create`` command, assuming
-you're on a machine where you can access the internet.
-
-The command will iterate through all of Spack's packages and download
-the safe ones into a directory structure like the one above.  Here is
-what it looks like:
-
-
-.. code-block:: bash
-
-   $ spack mirror create libelf libdwarf
-   ==> Created new mirror in spack-mirror-2014-06-24
-   ==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.13.tar.gz
-   ##########################################################                81.6%
-   ==> Checksum passed for libelf@0.8.13
-   ==> Added spack-mirror-2014-06-24/libelf/libelf-0.8.13.tar.gz to mirror
-   ==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.12.tar.gz
-   ######################################################################    98.6%
-   ==> Checksum passed for libelf@0.8.12
-   ==> Added spack-mirror-2014-06-24/libelf/libelf-0.8.12.tar.gz to mirror
-   ==> Trying to fetch from http://www.prevanders.net/libdwarf-20130207.tar.gz
-   ######################################################################    97.3%
-   ==> Checksum passed for libdwarf@20130207
-   ==> Added spack-mirror-2014-06-24/libdwarf/libdwarf-20130207.tar.gz to mirror
-   ==> Trying to fetch from http://www.prevanders.net/libdwarf-20130126.tar.gz
-   ########################################################                  78.9%
-   ==> Checksum passed for libdwarf@20130126
-   ==> Added spack-mirror-2014-06-24/libdwarf/libdwarf-20130126.tar.gz to mirror
-   ==> Trying to fetch from http://www.prevanders.net/libdwarf-20130729.tar.gz
-   #############################################################             84.7%
-   ==> Checksum passed for libdwarf@20130729
-   ==> Added spack-mirror-2014-06-24/libdwarf/libdwarf-20130729.tar.gz to mirror
-
-Once this is done, you can tar up the ``spack-mirror-2014-06-24`` directory and
-copy it over to the machine you want it hosted on.
-
-Custom package sets
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-Normally, ``spack mirror create`` downloads all the archives it has
-checksums for.  If you want to only create a mirror for a subset of
-packages, you can do that by supplying a list of package specs on the
-command line after ``spack mirror create``.  For example, this
-command::
-
-    $ spack mirror create libelf@0.8.12: boost@1.44:
-
-Will create a mirror for libelf versions greater than or equal to
-0.8.12 and boost versions greater than or equal to 1.44.
-
-Mirror files
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-If you have a *very* large number of packages you want to mirror, you
-can supply a file with specs in it, one per line::
-
-   $ cat specs.txt
-   libdwarf
-   libelf@0.8.12:
-   boost@1.44:
-   boost@1.39.0
-   ...
-   $ spack mirror create -f specs.txt
-   ...
-
-This is useful if there is a specific suite of software managed by
-your site.
-
-
-``spack mirror add``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Once you have a mirrror, you need to let spack know about it.  This is
-relatively simple.  First, figure out the URL for the mirror.  If it's
-a file, you can use a file URL like this one::
-
-    file:///Users/gamblin2/spack-mirror-2014-06-24
-
-That points to the directory on the local filesystem.  If it were on a
-web server, you could use a URL like this one:
-
-    https://example.com/some/web-hosted/directory/spack-mirror-2014-06-24
-
-Spack will use the URL as the root for all of the packages it fetches.
-You can tell your Spack installation to use that mirror like this:
-
-.. code-block:: bash
-
-   $ spack mirror add local_filesystem file:///Users/gamblin2/spack-mirror-2014-06-24
-
-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``::
-
-   $ spack mirror list
-   local_filesystem    file:///Users/gamblin2/spack-mirror-2014-06-24
-
-``spack mirror remove``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-And, if you want to remove a mirror, just remove it by name::
-
-   $ spack mirror remove local_filesystem
-   $ spack mirror list
-   ==> No mirrors configured.
-
-Mirror precedence
-~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Adding a mirror really just adds a section in ``~/.spackconfig``::
-
-   [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
-
-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.
-
-
 .. _temp-space:
 
 Temporary space
 ----------------------------
 
-.. warning:: Temporary space configuration will be moved to configuration files.
-   The intructions here are old and refer to ``__init__.py``
+.. 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
@@ -286,7 +94,7 @@ the virtual spec to specs for possible implementations, and
 later, so there is no need to fully concretize the spec when returning
 it.
 
-The ``DefaultConcretizer`` is intendend to provide sensible defaults
+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
@@ -327,3 +135,53 @@ Set concretizer to *your own* class instead of the default:
    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/env/cc

@@ -1,140 +1,332 @@
-#!/usr/bin/env python
-import sys
-if not sys.version_info[:2] >= (2,6):
-    sys.exit("Spack requires Python 2.6.  Version was %s." % sys.version_info)
+#!/bin/bash
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+#
+# Spack compiler wrapper script.
+#
+# Compiler commands go through this compiler wrapper in Spack builds.
+# The compiler wrapper is a thin layer around the standard compilers.
+# It enables several key pieces of functionality:
+#
+# 1. It allows Spack to swap compilers into and out of builds easily.
+# 2. It adds several options to the compile line so that spack
+#    packages can find their dependencies at build time and run time:
+#      -I           arguments for dependency /include directories.
+#      -L           arguments for dependency /lib directories.
+#      -Wl,-rpath   arguments for dependency /lib directories.
+#
 
-import os
-import re
-import subprocess
-from contextlib import closing
+# 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
+# as part of spack.package.Package.do_install().
+parameters="
+SPACK_PREFIX
+SPACK_ENV_PATH
+SPACK_DEBUG_LOG_DIR
+SPACK_COMPILER_SPEC
+SPACK_SHORT_SPEC"
 
-# Import spack parameters through the build environment.
-spack_lib = os.environ.get("SPACK_LIB")
-if not spack_lib:
-    print "Spack compiler must be run from spack!"
-    sys.exit(1)
+# 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:
+#   SPACK_DEBUG
+# Test command is used to unit test the compiler script.
+#   SPACK_TEST_COMMAND
+# Dependencies can be empty for pkgs with no deps:
+#   SPACK_DEPENDENCIES
 
-# Grab a minimal set of spack packages
-sys.path.append(spack_lib)
-from spack.compilation import *
-from external import argparse
-import llnl.util.tty as tty
+# die()
+# Prints a message and exits with error 1.
+function die {
+    echo "$@"
+    exit 1
+}
 
-spack_prefix        = get_env_var("SPACK_PREFIX")
-spack_debug         = get_env_flag("SPACK_DEBUG")
-spack_deps          = get_path("SPACK_DEPENDENCIES")
-spack_env_path      = get_path("SPACK_ENV_PATH")
-spack_debug_log_dir = get_env_var("SPACK_DEBUG_LOG_DIR")
-spack_spec          = get_env_var("SPACK_SPEC")
+for param in $parameters; do
+    if [ -z "${!param}" ]; then
+        die "Spack compiler must be run from spack!  Input $param was missing!"
+    fi
+done
 
-compiler_spec = get_env_var("SPACK_COMPILER_SPEC")
-spack_cc  = get_env_var("SPACK_CC",  required=False)
-spack_cxx = get_env_var("SPACK_CXX", required=False)
-spack_f77 = get_env_var("SPACK_F77", required=False)
-spack_fc  = get_env_var("SPACK_FC",  required=False)
+#
+# Figure out the type of compiler, the language, and the mode so that
+# the compiler script knows what to do.
+#
+# Possible languages are C, C++, Fortran 77, and Fortran 90.
+# 'command' is set based on the input command to $SPACK_[CC|CXX|F77|F90]
+#
+# 'mode' is set to one of:
+#    cc      compile
+#    ld      link
+#    ccld    compile & link
+#    cpp     preprocessor
+#    vcheck  version check
+#
+command=$(basename "$0")
+case "$command" in
+    cc|gcc|c89|c99|clang|xlc)
+        command="$SPACK_CC"
+        language="C"
+        ;;
+    c++|CC|g++|clang++|xlC)
+        command="$SPACK_CXX"
+        language="C++"
+        ;;
+    f77|xlf)
+        command="$SPACK_F77"
+        language="Fortran 77"
+        ;;
+    fc|f90|f95|xlf90)
+        command="$SPACK_FC"
+        language="Fortran 90"
+        ;;
+    cpp)
+        mode=cpp
+        ;;
+    ld)
+        mode=ld
+        ;;
+    *)
+        die "Unkown compiler: $command"
+        ;;
+esac
 
-# Figure out what type of operation we're doing
-command = os.path.basename(sys.argv[0])
+# Finish setting up the mode.
+if [ -z "$mode" ]; then
+    mode=ccld
+    for arg in "$@"; do
+        if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
+            mode=vcheck
+            break
+        elif [ "$arg" = -E ]; then
+            mode=cpp
+            break
+        elif [ "$arg" = -c ]; then
+            mode=cc
+            break
+        fi
+    done
+fi
 
-cpp, cc, ccld, ld, version_check = range(5)
+# Dump the version and exist if we're in testing mode.
+if [ "$SPACK_TEST_COMMAND" = "dump-mode" ]; then
+    echo "$mode"
+    exit
+fi
 
-if command == 'cpp':
-    mode = cpp
-elif command == 'ld':
-    mode = ld
-elif '-E' in sys.argv:
-    mode = cpp
-elif '-c' in sys.argv:
-    mode = cc
-else:
-    mode = ccld
+# Check that at least one of the real commands was actually selected,
+# otherwise we don't know what to execute.
+if [ -z "$command" ]; then
+    die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
+fi
 
+# Save original command for debug logging
+input_command="$@"
 
-if command in ('cc', 'gcc', 'c89', 'c99', 'clang'):
-    command = spack_cc
-    language = "C"
-elif command in ('c++', 'CC', 'g++', 'clang++'):
-    command = spack_cxx
-    language = "C++"
-elif command in ('f77'):
-    command = spack_f77
-    language = "Fortran 77"
-elif command in ('fc', 'f90', 'f95'):
-    command = spack_fc
-    language = "Fortran 90"
-elif command in ('ld', 'cpp'):
-    pass # leave it the same.  TODO: what's the right thing?
-else:
-    raise Exception("Unknown compiler: %s" % command)
+#
+# 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=()
 
-if command is None:
-    print "ERROR: Compiler '%s' does not support compiling %s programs." % (
-        compiler_spec, language)
-    sys.exit(1)
+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
 
-version_args = ['-V', '-v', '--version', '-dumpversion']
-if any(arg in sys.argv for arg in version_args):
-    mode = version_check
+# 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
 
-# Parse out the includes, libs, etc. so we can adjust them if need be.
-parser = argparse.ArgumentParser(add_help=False)
-parser.add_argument("-I", action='append', default=[], dest='include_path')
-parser.add_argument("-L", action='append', default=[], dest='lib_path')
-parser.add_argument("-l", action='append', default=[], dest='libs')
+# 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")
+    fi
 
-options, other_args = parser.parse_known_args()
-rpaths, other_args = parse_rpaths(other_args)
+    if [ -d "$dep/lib" ]; then
+        libraries+=("$dep/lib")
+        rpaths+=("$dep/lib")
+    fi
 
-# Add dependencies' include and lib paths to our compiler flags.
-def add_if_dir(path_list, directory, index=None):
-    if os.path.isdir(directory):
-        if index is None:
-            path_list.append(directory)
-        else:
-            path_list.insert(index, directory)
+    if [ -d "$dep/lib64" ]; then
+        libraries+=("$dep/lib64")
+        rpaths+=("$dep/lib64")
+    fi
+done
 
-for dep_dir in spack_deps:
-    add_if_dir(options.include_path, os.path.join(dep_dir, "include"))
-    add_if_dir(options.lib_path,     os.path.join(dep_dir, "lib"))
-    add_if_dir(options.lib_path,     os.path.join(dep_dir, "lib64"))
+# Include all -L's and prefix/whatever dirs in rpath
+for dir in "${libraries[@]}"; do
+    [[ dir = $SPACK_INSTALL* ]] && rpaths+=("$dir")
+done
+rpaths+=("$SPACK_PREFIX/lib")
+rpaths+=("$SPACK_PREFIX/lib64")
 
-# Add our modified arguments to it.
-arguments  = ['-I%s' % path for path in options.include_path]
-arguments += other_args
-arguments += ['-L%s' % path for path in options.lib_path]
-arguments += ['-l%s' % path for path in options.libs]
+# 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
 
-# Add rpaths to install dir and its dependencies.  We add both lib and lib64
-# here because we don't know which will be created.
-rpaths.extend(options.lib_path)
-rpaths.append('%s/lib'   % spack_prefix)
-rpaths.append('%s/lib64' % spack_prefix)
-if mode == ccld:
-    arguments += ['-Wl,-rpath,%s' % p for p in rpaths]
-elif mode == ld:
-    pairs = [('-rpath', '%s' % p) for p in rpaths]
-    arguments += [item for sublist in pairs for item in sublist]
+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
+fi
 
-# Unset some pesky environment variables
-for var in ["LD_LIBRARY_PATH", "LD_RUN_PATH", "DYLD_LIBRARY_PATH"]:
-    if var in os.environ:
-        os.environ.pop(var)
+#
+# Unset pesky environment variables that could affect build sanity.
+#
+unset LD_LIBRARY_PATH
+unset LD_RUN_PATH
+unset DYLD_LIBRARY_PATH
 
-# Ensure that the delegated command doesn't just call this script again.
-remove_paths = ['.'] + spack_env_path
-path = [p for p in get_path("PATH") if p not in remove_paths]
-os.environ["PATH"] = ":".join(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] + arguments
+full_command=("$command")
+full_command+=("${args[@]}")
 
-if spack_debug:
-    input_log = os.path.join(spack_debug_log_dir,  'spack-cc-%s.in.log' % spack_spec)
-    output_log = os.path.join(spack_debug_log_dir, 'spack-cc-%s.out.log' % spack_spec)
-    with closing(open(input_log, 'a')) as log:
-        args = [os.path.basename(sys.argv[0])] + sys.argv[1:]
-        log.write("%s\n" % " ".join(arg.replace(' ', r'\ ') for arg in args))
-    with closing(open(output_log, 'a')) as log:
-        log.write("%s\n" % " ".join(full_command))
+#
+# Write the input and output commands to debug logs if it's asked for.
+#
+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
+fi
 
-rcode = subprocess.call(full_command)
-sys.exit(rcode)
+exec "${full_command[@]}"

lib/spack/env/clang

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

lib/spack/env/clang++

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

lib/spack/env/g++

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

lib/spack/env/gcc

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

lib/spack/external/argparse.py

@@ -1708,6 +1708,21 @@ def _add_action(self, action):
             self._positionals._add_action(action)
         return action
 
+
+    def get_subparser(self, name):
+        """Gets a subparser added with the supplied name.
+           This is an extension to the standard argparse API.
+        """
+        subpasrsers_actions = [
+            action for action in self._actions
+            if isinstance(action, _SubParsersAction)]
+        for action in subpasrsers_actions:
+            for choice, subparser in action.choices.items():
+                if choice == name:
+                    return subparser
+        return None
+
+
     def _get_optional_actions(self):
         return [action
                 for action in self._actions

lib/spack/llnl/util/filesystem.py

@@ -22,13 +22,16 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-__all__ = ['install', 'expand_user', 'working_dir', 'touch', 'mkdirp',
-           'join_path', 'ancestor', 'can_access', 'filter_file', 'change_sed_delimiter']
+__all__ = ['set_install_permissions', 'install', 'install_tree', 'traverse_tree',
+           'expand_user', 'working_dir', 'touch', 'touchp', 'mkdirp',
+           'force_remove', 'join_path', 'ancestor', 'can_access', 'filter_file',
+           'change_sed_delimiter', 'is_exe', 'force_symlink']
 
 import os
 import sys
 import re
 import shutil
+import stat
 import errno
 import getpass
 from contextlib import contextmanager, closing
@@ -62,8 +65,11 @@ def filter_file(regex, repl, *filenames, **kwargs):
     # Allow strings to use \1, \2, etc. for replacement, like sed
     if not callable(repl):
         unescaped = repl.replace(r'\\', '\\')
-        repl = lambda m: re.sub(
-            r'\\([0-9])', lambda x: m.group(int(x.group(1))), unescaped)
+        def replace_groups_with_groupid(m):
+            def groupid_to_group(x):
+                return m.group(int(x.group(1)))
+            return re.sub(r'\\([1-9])', groupid_to_group, unescaped)
+        repl = replace_groups_with_groupid
 
     if string:
         regex = re.escape(regex)
@@ -127,10 +133,44 @@ def change_sed_delimiter(old_delim, new_delim, *filenames):
         filter_file(double_quoted, '"%s"' % repl, f)
 
 
+def set_install_permissions(path):
+    """Set appropriate permissions on the installed file."""
+    if os.path.isdir(path):
+        os.chmod(path, 0755)
+    else:
+        os.chmod(path, 0644)
+
+
+def copy_mode(src, dest):
+    src_mode = os.stat(src).st_mode
+    dest_mode = os.stat(dest).st_mode
+    if src_mode | stat.S_IXUSR: dest_mode |= stat.S_IXUSR
+    if src_mode | stat.S_IXGRP: dest_mode |= stat.S_IXGRP
+    if src_mode | stat.S_IXOTH: dest_mode |= stat.S_IXOTH
+    os.chmod(dest, dest_mode)
+
+
 def install(src, dest):
     """Manually install a file to a particular location."""
     tty.info("Installing %s to %s" % (src, dest))
     shutil.copy(src, dest)
+    set_install_permissions(dest)
+    copy_mode(src, dest)
+
+
+def install_tree(src, dest, **kwargs):
+    """Manually install a file to a particular location."""
+    tty.info("Installing %s to %s" % (src, dest))
+    shutil.copytree(src, dest, **kwargs)
+
+    for s, d in traverse_tree(src, dest, follow_nonexisting=False):
+        set_install_permissions(d)
+        copy_mode(s, d)
+
+
+def is_exe(path):
+    """True if path is an executable file."""
+    return os.path.isfile(path) and os.access(path, os.X_OK)
 
 
 def expand_user(path):
@@ -152,6 +192,15 @@ def mkdirp(*paths):
             raise OSError(errno.EEXIST, "File alredy exists", path)
 
 
+def force_remove(*paths):
+    """Remove files without printing errors.  Like rm -f, does NOT
+       remove directories."""
+    for path in paths:
+        try:
+            os.remove(path)
+        except OSError, e:
+            pass
+
 @contextmanager
 def working_dir(dirname, **kwargs):
     if kwargs.get('create', False):
@@ -169,6 +218,20 @@ def touch(path):
         os.utime(path, None)
 
 
+def touchp(path):
+    """Like touch, but creates any parent directories needed for the file."""
+    mkdirp(os.path.dirname(path))
+    touch(path)
+
+
+def force_symlink(src, dest):
+    try:
+        os.symlink(src, dest)
+    except OSError, e:
+        os.remove(dest)
+        os.symlink(src, dest)
+
+
 def join_path(prefix, *args):
     path = str(prefix)
     for elt in args:
@@ -187,3 +250,84 @@ def ancestor(dir, n=1):
 def can_access(file_name):
     """True if we have read/write access to the file."""
     return os.access(file_name, os.R_OK|os.W_OK)
+
+
+def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
+    """Traverse two filesystem trees simultaneously.
+
+    Walks the LinkTree directory in pre or post order.  Yields each
+    file in the source directory with a matching path from the dest
+    directory, along with whether the file is a directory.
+    e.g., for this tree::
+
+        root/
+          a/
+            file1
+            file2
+          b/
+            file3
+
+    When called on dest, this yields::
+
+        ('root',         'dest')
+        ('root/a',       'dest/a')
+        ('root/a/file1', 'dest/a/file1')
+        ('root/a/file2', 'dest/a/file2')
+        ('root/b',       'dest/b')
+        ('root/b/file3', 'dest/b/file3')
+
+    Optional args:
+
+    order=[pre|post] -- Whether to do pre- or post-order traveral.
+
+    ignore=<predicate> -- Predicate indicating which files to ignore.
+
+    follow_nonexisting -- Whether to descend into directories in
+                          src that do not exit in dest. Default True.
+
+    follow_links -- Whether to descend into symlinks in src.
+
+    """
+    follow_nonexisting = kwargs.get('follow_nonexisting', True)
+    follow_links = kwargs.get('follow_link', False)
+
+    # Yield in pre or post order?
+    order  = kwargs.get('order', 'pre')
+    if order not in ('pre', 'post'):
+        raise ValueError("Order must be 'pre' or 'post'.")
+
+    # List of relative paths to ignore under the src root.
+    ignore = kwargs.get('ignore', lambda filename: False)
+
+    # Don't descend into ignored directories
+    if ignore(rel_path):
+        return
+
+    source_path = os.path.join(source_root, rel_path)
+    dest_path   = os.path.join(dest_root, rel_path)
+
+    # preorder yields directories before children
+    if order == 'pre':
+        yield (source_path, dest_path)
+
+    for f in os.listdir(source_path):
+        source_child = os.path.join(source_path, f)
+        dest_child   = os.path.join(dest_path, f)
+        rel_child    = os.path.join(rel_path, f)
+
+        # Treat as a directory
+        if os.path.isdir(source_child) and (
+            follow_links or not os.path.islink(source_child)):
+
+            # When follow_nonexisting isn't set, don't descend into dirs
+            # in source that do not exist in dest
+            if follow_nonexisting or os.path.exists(dest_child):
+                tuples = traverse_tree(source_root, dest_root, rel_child, **kwargs)
+                for t in tuples: yield t
+
+        # Treat as a file.
+        elif not ignore(os.path.join(rel_path, f)):
+            yield (source_child, dest_child)
+
+    if order == 'post':
+        yield (source_path, dest_path)

lib/spack/llnl/util/lang.py

@@ -68,6 +68,12 @@ def index_by(objects, *funcs):
 
            index1 = index_by(list_of_specs, 'arch', 'compiler')
            index2 = index_by(list_of_specs, 'compiler')
+
+       You can also index by tuples by passing tuples:
+
+           index1 = index_by(list_of_specs, ('arch', 'compiler'))
+
+       Keys in the resulting dict will look like ('gcc', 'bgqos_0').
     """
     if not funcs:
         return objects
@@ -75,6 +81,8 @@ def index_by(objects, *funcs):
     f = funcs[0]
     if isinstance(f, basestring):
         f = lambda x: getattr(x, funcs[0])
+    elif isinstance(f, tuple):
+        f = lambda x: tuple(getattr(x, p) for p in funcs[0])
 
     result = {}
     for o in objects:
@@ -261,6 +269,59 @@ def in_function(function_name):
         del stack
 
 
+def check_kwargs(kwargs, fun):
+    """Helper for making functions with kwargs.  Checks whether the kwargs
+       are empty after all of them have been popped off.  If they're
+       not, raises an error describing which kwargs are invalid.
+
+       Example::
+
+          def foo(self, **kwargs):
+              x = kwargs.pop('x', None)
+              y = kwargs.pop('y', None)
+              z = kwargs.pop('z', None)
+              check_kwargs(kwargs, self.foo)
+
+          # This raises a TypeError:
+          foo(w='bad kwarg')
+    """
+    if kwargs:
+        raise TypeError(
+            "'%s' is an invalid keyword argument for function %s()."
+            % (next(kwargs.iterkeys()), fun.__name__))
+
+
+def match_predicate(*args):
+    """Utility function for making string matching predicates.
+
+    Each arg can be a:
+        - regex
+        - list or tuple of regexes
+        - predicate that takes a string.
+
+    This returns a predicate that is true if:
+        - any arg regex matches
+        - any regex in a list or tuple of regexes matches.
+        - any predicate in args matches.
+    """
+    def match(string):
+        for arg in args:
+            if isinstance(arg, basestring):
+                if re.search(arg, string):
+                    return True
+            elif isinstance(arg, list) or isinstance(arg, tuple):
+                if any(re.search(i, string) for i in arg):
+                    return True
+            elif callable(arg):
+                if arg(string):
+                    return True
+            else:
+                raise ValueError("args to match_predicate must be regex, "
+                                 "list of regexes, or callable.")
+        return False
+    return match
+
+
 class RequiredAttributeError(ValueError):
     def __init__(self, message):
         super(RequiredAttributeError, self).__init__(message)

lib/spack/llnl/util/link_tree.py

@@ -0,0 +1,115 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+"""LinkTree class for setting up trees of symbolic links."""
+__all__ = ['LinkTree']
+
+import os
+import shutil
+from llnl.util.filesystem import *
+
+empty_file_name = '.spack-empty'
+
+
+class LinkTree(object):
+    """Class to create trees of symbolic links from a source directory.
+
+    LinkTree objects are constructed with a source root.  Their
+    methods allow you to create and delete trees of symbolic links
+    back to the source tree in specific destination directories.
+    Trees comprise symlinks only to files; directries are never
+    symlinked to, to prevent the source directory from ever being
+    modified.
+
+    """
+    def __init__(self, source_root):
+        if not os.path.exists(source_root):
+            raise IOError("No such file or directory: '%s'", source_root)
+
+        self._root = source_root
+
+
+    def find_conflict(self, dest_root, **kwargs):
+        """Returns the first file in dest that conflicts with src"""
+        kwargs['follow_nonexisting'] = False
+        for src, dest in traverse_tree(self._root, dest_root, **kwargs):
+            if os.path.isdir(src):
+                if os.path.exists(dest) and not os.path.isdir(dest):
+                    return dest
+            elif os.path.exists(dest):
+                return dest
+        return None
+
+
+    def merge(self, dest_root, **kwargs):
+        """Link all files in src into dest, creating directories if necessary."""
+        kwargs['order'] = 'pre'
+        for src, dest in traverse_tree(self._root, dest_root, **kwargs):
+            if os.path.isdir(src):
+                if not os.path.exists(dest):
+                    mkdirp(dest)
+                    continue
+
+                if not os.path.isdir(dest):
+                    raise ValueError("File blocks directory: %s" % dest)
+
+                # mark empty directories so they aren't removed on unmerge.
+                if not os.listdir(dest):
+                    marker = os.path.join(dest, empty_file_name)
+                    touch(marker)
+
+            else:
+                assert(not os.path.exists(dest))
+                os.symlink(src, dest)
+
+
+    def unmerge(self, dest_root, **kwargs):
+        """Unlink all files in dest that exist in src.
+
+        Unlinks directories in dest if they are empty.
+
+        """
+        kwargs['order'] = 'post'
+        for src, dest in traverse_tree(self._root, dest_root, **kwargs):
+            if os.path.isdir(src):
+                # Skip non-existing links.
+                if not os.path.exists(dest):
+                    continue
+
+                if not os.path.isdir(dest):
+                    raise ValueError("File blocks directory: %s" % dest)
+
+                # remove directory if it is empty.
+                if not os.listdir(dest):
+                    shutil.rmtree(dest, ignore_errors=True)
+
+                # remove empty dir marker if present.
+                marker = os.path.join(dest, empty_file_name)
+                if os.path.exists(marker):
+                    os.remove(marker)
+
+            elif os.path.exists(dest):
+                if not os.path.islink(dest):
+                    raise ValueError("%s is not a link tree!" % dest)
+                os.remove(dest)

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

@@ -25,6 +25,9 @@
 import sys
 import os
 import textwrap
+import fcntl
+import termios
+import struct
 from StringIO import StringIO
 
 from llnl.util.tty.color import *
@@ -114,21 +117,46 @@ def get_number(prompt, **kwargs):
     return number
 
 
+def get_yes_or_no(prompt, **kwargs):
+    default_value = kwargs.get('default', None)
+
+    if default_value is None:
+        prompt += ' [y/n] '
+    elif default_value is True:
+        prompt += ' [Y/n] '
+    elif default_value is False:
+        prompt += ' [y/N] '
+    else:
+        raise ValueError("default for get_yes_no() must be True, False, or None.")
+
+    result = None
+    while result is None:
+        ans = raw_input(prompt).lower()
+        if not ans:
+            result = default_value
+            if result is None:
+                print "Please enter yes or no."
+        else:
+            if ans == 'y' or ans == 'yes':
+                result = True
+            elif ans == 'n' or ans == 'no':
+                result = False
+    return result
+
+
 def hline(label=None, **kwargs):
-    """Draw an optionally colored or labeled horizontal line.
+    """Draw a labeled horizontal line.
        Options:
-
        char       Char to draw the line with.  Default '-'
-       color      Color of the label.  Default is no color.
        max_width  Maximum width of the line.  Default is 64 chars.
-
-       See tty.color for possible color formats.
     """
-    char      = kwargs.get('char', '-')
-    color     = kwargs.get('color', '')
-    max_width = kwargs.get('max_width', 64)
+    char      = kwargs.pop('char', '-')
+    max_width = kwargs.pop('max_width', 64)
+    if kwargs:
+        raise TypeError("'%s' is an invalid keyword argument for this function."
+                        % next(kwargs.iterkeys()))
 
-    cols, rows = terminal_size()
+    rows, cols = terminal_size()
     if not cols:
         cols = max_width
     else:
@@ -136,37 +164,34 @@ def hline(label=None, **kwargs):
     cols = min(max_width, cols)
 
     label = str(label)
-    prefix = char * 2 + " " + label + " "
-    suffix = (cols - len(prefix)) * char
+    prefix = char * 2 + " "
+    suffix = " " + (cols - len(prefix) - clen(label)) * char
 
     out = StringIO()
-    if color:
-        prefix = char * 2 + " " + color + cescape(label) + "@. "
-        cwrite(prefix, stream=out, color=True)
-    else:
-        out.write(prefix)
+    out.write(prefix)
+    out.write(label)
     out.write(suffix)
 
     print out.getvalue()
 
 
 def terminal_size():
-    """Gets the dimensions of the console: cols, rows."""
+    """Gets the dimensions of the console: (rows, cols)."""
     def ioctl_GWINSZ(fd):
         try:
-            cr = struct.unpack('hh', fcntl.ioctl(fd, termios.TIOCGWINSZ, '1234'))
+            rc = struct.unpack('hh', fcntl.ioctl(fd, termios.TIOCGWINSZ, '1234'))
         except:
             return
-        return cr
-    cr = ioctl_GWINSZ(0) or ioctl_GWINSZ(1) or ioctl_GWINSZ(2)
-    if not cr:
+        return rc
+    rc = ioctl_GWINSZ(0) or ioctl_GWINSZ(1) or ioctl_GWINSZ(2)
+    if not rc:
         try:
             fd = os.open(os.ctermid(), os.O_RDONLY)
-            cr = ioctl_GWINSZ(fd)
+            rc = ioctl_GWINSZ(fd)
             os.close(fd)
         except:
             pass
-    if not cr:
-        cr = (os.environ.get('LINES', 25), os.environ.get('COLUMNS', 80))
+    if not rc:
+        rc = (os.environ.get('LINES', 25), os.environ.get('COLUMNS', 80))
 
-    return int(cr[1]), int(cr[0])
+    return int(rc[0]), int(rc[1])

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

@@ -22,16 +22,9 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-# colify
-# By Todd Gamblin, tgamblin@llnl.gov
-#
-# Takes a list of items as input and finds a good columnization of them,
-# similar to how gnu ls does.  You can pipe output to this script and
-# get a tight display for it.  This supports both uniform-width and
-# variable-width (tighter) columns.
-#
-# Run colify -h for more information.
-#
+"""
+Routines for printing columnar output.  See colify() for more information.
+"""
 import os
 import sys
 import fcntl
@@ -40,6 +33,7 @@
 from StringIO import StringIO
 
 from llnl.util.tty import terminal_size
+from llnl.util.tty.color import clen
 
 
 class ColumnConfig:
@@ -47,32 +41,52 @@ def __init__(self, cols):
         self.cols = cols
         self.line_length = 0
         self.valid = True
-        self.widths = [0] * cols
+        self.widths = [0] * cols   # does not include ansi colors
+        self.cwidths = [0] * cols  # includes ansi colors
 
     def __repr__(self):
         attrs = [(a,getattr(self, a)) for a in dir(self) if not a.startswith("__")]
         return "<Config: %s>" % ", ".join("%s: %r" % a for a in attrs)
 
 
-def config_variable_cols(elts, console_cols, padding):
+def config_variable_cols(elts, console_width, padding, cols=0):
+    """Variable-width column fitting algorithm.
+
+       This function determines the most columns that can fit in the
+       screen width.  Unlike uniform fitting, where all columns take
+       the width of the longest element in the list, each column takes
+       the width of its own longest element. This packs elements more
+       efficiently on screen.
+
+       If cols is nonzero, force
+    """
+    if cols < 0:
+        raise ValueError("cols must be non-negative.")
+
     # Get a bound on the most columns we could possibly have.
-    lengths = [len(elt) for elt in elts]
-    max_cols = max(1, console_cols / (min(lengths) + padding))
+    # 'clen' ignores length of ansi color sequences.
+    lengths = [clen(e) for e in elts]
+    clengths = [len(e) for e in elts]
+
+    max_cols = max(1, console_width / (min(lengths) + padding))
     max_cols = min(len(elts), max_cols)
 
-    configs = [ColumnConfig(c) for c in xrange(1, max_cols+1)]
-    for elt, length in enumerate(lengths):
-        for i, conf in enumerate(configs):
-            if conf.valid:
-                col = elt / ((len(elts) + i) / (i + 1))
-                padded = length
-                if col < i:
-                    padded += padding
+    # Range of column counts to try.  If forced, use the supplied value.
+    col_range = [cols] if cols else xrange(1, max_cols+1)
 
-                if conf.widths[col] < padded:
-                    conf.line_length += padded - conf.widths[col]
-                    conf.widths[col] = padded
-                    conf.valid = (conf.line_length < console_cols)
+    # Determine the most columns possible for the console width.
+    configs = [ColumnConfig(c) for c in col_range]
+    for i, length in enumerate(lengths):
+        for conf in configs:
+            if conf.valid:
+                col = i / ((len(elts) + conf.cols - 1) / conf.cols)
+                p = padding if col < (conf.cols - 1) else 0
+
+                if conf.widths[col] < (length + p):
+                    conf.line_length += length + p - conf.widths[col]
+                    conf.widths[col]  = length + p
+                    conf.cwidths[col] = clengths[i] + p
+                    conf.valid = (conf.line_length < console_width)
 
     try:
         config = next(conf for conf in reversed(configs) if conf.valid)
@@ -85,57 +99,107 @@ def config_variable_cols(elts, console_cols, padding):
     return config
 
 
-def config_uniform_cols(elts, console_cols, padding):
-    max_len = max(len(elt) for elt in elts) + padding
-    cols = max(1, console_cols / max_len)
-    cols = min(len(elts), cols)
+def config_uniform_cols(elts, console_width, padding, cols=0):
+    """Uniform-width column fitting algorithm.
+
+       Determines the longest element in the list, and determines how
+       many columns of that width will fit on screen.  Returns a
+       corresponding column config.
+    """
+    if cols < 0:
+        raise ValueError("cols must be non-negative.")
+
+    # 'clen' ignores length of ansi color sequences.
+    max_len = max(clen(e) for e in elts) + padding
+    max_clen = max(len(e) for e in elts) + padding
+    if cols == 0:
+        cols = max(1, console_width / max_len)
+        cols = min(len(elts), cols)
+
     config = ColumnConfig(cols)
     config.widths = [max_len] * cols
+    config.cwidths = [max_clen] * cols
+
     return config
 
 
-def isatty(ostream):
-    force = os.environ.get('COLIFY_TTY', 'false').lower() != 'false'
-    return force or ostream.isatty()
-
-
 def colify(elts, **options):
+    """Takes a list of elements as input and finds a good columnization
+    of them, similar to how gnu ls does. This supports both
+    uniform-width and variable-width (tighter) columns.
+
+    If elts is not a list of strings, each element is first conveted
+    using str().
+
+    Keyword arguments:
+
+    output=<stream>   A file object to write to.  Default is sys.stdout.
+    indent=<int>      Optionally indent all columns by some number of spaces.
+    padding=<int>     Spaces between columns.  Default is 2.
+    width=<int>       Width of the output.  Default is 80 if tty is not detected.
+
+    cols=<int>        Force number of columns. Default is to size to terminal,
+                      or single-column if no tty
+
+    tty=<bool>        Whether to attempt to write to a tty.  Default is to
+                      autodetect a tty. Set to False to force single-column output.
+
+    method=<string>   Method to use to fit columns.  Options are variable or uniform.
+                      Variable-width columns are tighter, uniform columns are all the
+                      same width and fit less data on the screen.
+
+    len=<func>        Function to use for calculating string length.
+                      Useful for ignoring ansi color. Default is 'len'.
+    """
     # Get keyword arguments or set defaults
-    output       = options.get("output", sys.stdout)
-    indent       = options.get("indent", 0)
-    padding      = options.get("padding", 2)
-    tty          = options.get('tty', None)
+    cols         = options.pop("cols", 0)
+    output       = options.pop("output", sys.stdout)
+    indent       = options.pop("indent", 0)
+    padding      = options.pop("padding", 2)
+    tty          = options.pop('tty', None)
+    method       = options.pop("method", "variable")
+    console_cols = options.pop("width", None)
+
+    if options:
+        raise TypeError("'%s' is an invalid keyword argument for this function."
+                        % next(options.iterkeys()))
 
     # elts needs to be an array of strings so we can count the elements
     elts = [str(elt) for elt in elts]
     if not elts:
         return (0, ())
 
+    # environment size is of the form "<rows>x<cols>"
+    env_size = os.environ.get('COLIFY_SIZE')
+    if env_size:
+        try:
+            r, c = env_size.split('x')
+            console_rows, console_cols = int(r), int(c)
+            tty = True
+        except: pass
+
+    # Use only one column if not a tty.
     if not tty:
-        if tty is False or not isatty(output):
-            for elt in elts:
-                output.write("%s\n" % elt)
+        if tty is False or not output.isatty():
+            cols = 1
 
-            maxlen = max(len(str(s)) for s in elts)
-            return (1, (maxlen,))
-
-    console_cols = options.get("cols", None)
+    # Specify the number of character columns to use.
     if not console_cols:
-        console_cols, console_rows = terminal_size()
+        console_rows, console_cols = terminal_size()
     elif type(console_cols) != int:
         raise ValueError("Number of columns must be an int")
     console_cols = max(1, console_cols - indent)
 
-    method = options.get("method", "variable")
+    # Choose a method.  Variable-width colums vs uniform-width.
     if method == "variable":
-        config = config_variable_cols(elts, console_cols, padding)
+        config = config_variable_cols(elts, console_cols, padding, cols)
     elif method == "uniform":
-        config = config_uniform_cols(elts, console_cols, padding)
+        config = config_uniform_cols(elts, console_cols, padding, cols)
     else:
         raise ValueError("method must be one of: " + allowed_methods)
 
     cols = config.cols
-    formats = ["%%-%ds" % width for width in config.widths[:-1]]
+    formats = ["%%-%ds" % width for width in config.cwidths[:-1]]
     formats.append("%s")  # last column has no trailing space
 
     rows = (len(elts) + cols - 1) / cols
@@ -155,6 +219,25 @@ def colify(elts, **options):
     return (config.cols, tuple(config.widths))
 
 
+def colify_table(table, **options):
+    if table is None:
+        raise TypeError("Can't call colify_table on NoneType")
+    elif not table or not table[0]:
+        raise ValueError("Table is empty in colify_table!")
+
+    columns = len(table[0])
+    def transpose():
+        for i in xrange(columns):
+            for row in table:
+                yield row[i]
+
+    if 'cols' in options:
+        raise ValueError("Cannot override columsn in colify_table.")
+    options['cols'] = columns
+
+    colify(transpose(), **options)
+
+
 def colified(elts, **options):
     """Invokes the colify() function but returns the result as a string
        instead of writing it to an output string."""
@@ -162,29 +245,3 @@ def colified(elts, **options):
     options['output'] = sio
     colify(elts, **options)
     return sio.getvalue()
-
-
-if __name__ == "__main__":
-    import optparse
-
-    cols, rows = terminal_size()
-    parser = optparse.OptionParser()
-    parser.add_option("-u", "--uniform", action="store_true", default=False,
-                      help="Use uniformly sized columns instead of variable-size.")
-    parser.add_option("-p", "--padding", metavar="PADDING", action="store",
-                      type=int, default=2, help="Spaces to add between columns.  Default is 2.")
-    parser.add_option("-i", "--indent", metavar="SPACES", action="store",
-                      type=int, default=0, help="Indent the output by SPACES.  Default is 0.")
-    parser.add_option("-w", "--width", metavar="COLS", action="store",
-                      type=int, default=cols, help="Indent the output by SPACES.  Default is 0.")
-    options, args = parser.parse_args()
-
-    method = "variable"
-    if options.uniform:
-        method = "uniform"
-
-    if sys.stdin.isatty():
-        parser.print_help()
-        sys.exit(1)
-    else:
-        colify([line.strip() for line in sys.stdin], method=method, **options.__dict__)

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

@@ -149,6 +149,11 @@ def colorize(string, **kwargs):
     return re.sub(color_re, match_to_ansi(color), string)
 
 
+def clen(string):
+    """Return the length of a string, excluding ansi color sequences."""
+    return len(re.sub(r'\033[^m]*m', '', string))
+
+
 def cwrite(string, stream=sys.stdout, color=None):
     """Replace all color expressions in string with ANSI control
        codes and write the result to the stream.  If color is
@@ -172,17 +177,20 @@ def cescape(string):
 
 class ColorStream(object):
     def __init__(self, stream, color=None):
-        self.__class__ = type(stream.__class__.__name__,
-                              (self.__class__, stream.__class__), {})
-        self.__dict__ = stream.__dict__
-        self.color = color
-        self.stream = stream
+        self._stream = stream
+        self._color = color
 
     def write(self, string, **kwargs):
-        if kwargs.get('raw', False):
-            super(ColorStream, self).write(string)
-        else:
-            cwrite(string, self.stream, self.color)
+        raw = kwargs.get('raw', False)
+        raw_write = getattr(self._stream, 'write')
+
+        color = self._color
+        if self._color is None:
+            if raw:
+                color=True
+            else:
+                color = self._stream.isatty()
+        raw_write(colorize(string, color=color))
 
     def writelines(self, sequence, **kwargs):
         raw = kwargs.get('raw', False)

lib/spack/spack/__init__.py

@@ -26,7 +26,7 @@
 import tempfile
 from llnl.util.filesystem import *
 
-# This lives in $prefix/lib/spac/spack/__file__
+# This lives in $prefix/lib/spack/spack/__file__
 prefix = ancestor(__file__, 4)
 
 # The spack script itself
@@ -78,7 +78,7 @@
 
 # Version information
 from spack.version import Version
-spack_version = Version("0.8")
+spack_version = Version("0.8.15")
 
 #
 # Executables used by Spack
@@ -138,7 +138,7 @@
 #       should live.  This file is overloaded for spack core vs. for packages.
 #
 __all__ = ['Package', 'Version', 'when', 'ver']
-from spack.package import Package
+from spack.package import Package, ExtensionConflictError
 from spack.version import Version, ver
 from spack.multimethod import when
 

lib/spack/spack/architecture.py

@@ -65,7 +65,7 @@ def get_mac_sys_type():
     if not mac_ver:
         return None
 
-    return "macosx_{}_{}".format(
+    return "macosx_%s_%s" % (
         Version(mac_ver).up_to(2), py_platform.machine())
 
 

lib/spack/spack/build_environment.py

@@ -28,6 +28,7 @@
 calls you can make from within the install() function.
 """
 import os
+import sys
 import shutil
 import multiprocessing
 import platform
@@ -48,12 +49,12 @@
 # set_build_environment_variables and used to pass parameters to
 # Spack's compiler wrappers.
 #
-SPACK_LIB              = 'SPACK_LIB'
 SPACK_ENV_PATH         = 'SPACK_ENV_PATH'
 SPACK_DEPENDENCIES     = 'SPACK_DEPENDENCIES'
 SPACK_PREFIX           = 'SPACK_PREFIX'
+SPACK_INSTALL          = 'SPACK_INSTALL'
 SPACK_DEBUG            = 'SPACK_DEBUG'
-SPACK_SPEC             = 'SPACK_SPEC'
+SPACK_SHORT_SPEC       = 'SPACK_SHORT_SPEC'
 SPACK_DEBUG_LOG_DIR    = 'SPACK_DEBUG_LOG_DIR'
 
 
@@ -67,16 +68,16 @@ class MakeExecutable(Executable):
        Note that if the SPACK_NO_PARALLEL_MAKE env var is set it overrides
        everything.
     """
-    def __init__(self, name, parallel):
+    def __init__(self, name, jobs):
         super(MakeExecutable, self).__init__(name)
-        self.parallel = parallel
+        self.jobs = jobs
 
     def __call__(self, *args, **kwargs):
-        parallel = kwargs.get('parallel', self.parallel)
+        parallel = kwargs.get('parallel', self.jobs > 1)
         disable_parallel = env_flag(SPACK_NO_PARALLEL_MAKE)
 
-        if parallel and not disable_parallel:
-            jobs = "-j%d" % multiprocessing.cpu_count()
+        if self.jobs > 1 and not disable_parallel:
+            jobs = "-j%d" % self.jobs
             args = (jobs,) + args
 
         super(MakeExecutable, self).__call__(*args, **kwargs)
@@ -108,9 +109,6 @@ def set_compiler_environment_variables(pkg):
 def set_build_environment_variables(pkg):
     """This ensures a clean install environment when we build packages.
     """
-    # This tells the compiler script where to find the Spack installation.
-    os.environ[SPACK_LIB] = spack.lib_path
-
     # Add spack build environment path with compiler wrappers first in
     # the path.  We handle case sensitivity conflicts like "CC" and
     # "cc" by putting one in the <build_env_path>/case-insensitive
@@ -128,6 +126,9 @@ def set_build_environment_variables(pkg):
     # Install prefix
     os.environ[SPACK_PREFIX] = pkg.prefix
 
+    # Install root prefix
+    os.environ[SPACK_INSTALL] = spack.install_path
+
     # Remove these vars from the environment during build becaus they
     # can affect how some packages find libraries.  We want to make
     # sure that builds never pull in unintended external dependencies.
@@ -140,7 +141,7 @@ def set_build_environment_variables(pkg):
     # Working directory for the spack command itself, for debug logs.
     if spack.debug:
         os.environ[SPACK_DEBUG] = "TRUE"
-    os.environ[SPACK_SPEC] = str(pkg.spec)
+    os.environ[SPACK_SHORT_SPEC] = pkg.spec.short_spec
     os.environ[SPACK_DEBUG_LOG_DIR] = spack.spack_working_dir
 
     # Add dependencies to CMAKE_PREFIX_PATH
@@ -162,15 +163,21 @@ def set_module_variables_for_package(pkg):
     """
     m = pkg.module
 
-    m.make  = MakeExecutable('make', pkg.parallel)
-    m.gmake = MakeExecutable('gmake', pkg.parallel)
+    # number of jobs spack will to build with.
+    jobs = multiprocessing.cpu_count()
+    if not pkg.parallel:
+        jobs = 1
+    elif pkg.make_jobs:
+        jobs = pkg.make_jobs
+    m.make_jobs = jobs
+
+    # TODO: make these build deps that can be installed if not found.
+    m.make  = MakeExecutable('make', jobs)
+    m.gmake = MakeExecutable('gmake', jobs)
 
     # easy shortcut to os.environ
     m.env = os.environ
 
-    # number of jobs spack prefers to build with.
-    m.make_jobs = multiprocessing.cpu_count()
-
     # Find the configure script in the archive path
     # Don't use which for this; we want to find it in the current dir.
     m.configure = Executable('./configure')
@@ -187,19 +194,102 @@ def set_module_variables_for_package(pkg):
     if platform.mac_ver()[0]:
         m.std_cmake_args.append('-DCMAKE_FIND_FRAMEWORK=LAST')
 
-    # Emulate some shell commands for convenience
-    m.pwd        = os.getcwd
-    m.cd         = os.chdir
-    m.mkdir      = os.mkdir
-    m.makedirs   = os.makedirs
-    m.remove     = os.remove
-    m.removedirs = os.removedirs
+    # Set up CMake rpath
+    m.std_cmake_args.append('-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE')
+    m.std_cmake_args.append('-DCMAKE_INSTALL_RPATH=%s' % ":".join(get_rpaths(pkg)))
 
-    m.mkdirp     = mkdirp
-    m.install    = install
-    m.rmtree     = shutil.rmtree
-    m.move       = shutil.move
+    # Emulate some shell commands for convenience
+    m.pwd          = os.getcwd
+    m.cd           = os.chdir
+    m.mkdir        = os.mkdir
+    m.makedirs     = os.makedirs
+    m.remove       = os.remove
+    m.removedirs   = os.removedirs
+    m.symlink      = os.symlink
+
+    m.mkdirp       = mkdirp
+    m.install      = install
+    m.install_tree = install_tree
+    m.rmtree       = shutil.rmtree
+    m.move         = shutil.move
 
     # Useful directories within the prefix are encapsulated in
     # a Prefix object.
     m.prefix  = pkg.prefix
+
+
+def get_rpaths(pkg):
+    """Get a list of all the rpaths for a package."""
+    rpaths = [pkg.prefix.lib, pkg.prefix.lib64]
+    rpaths.extend(d.prefix.lib for d in pkg.spec.traverse(root=False)
+                  if os.path.isdir(d.prefix.lib))
+    rpaths.extend(d.prefix.lib64 for d in pkg.spec.traverse(root=False)
+                  if os.path.isdir(d.prefix.lib64))
+    return rpaths
+
+
+def setup_package(pkg):
+    """Execute all environment setup routines."""
+    set_compiler_environment_variables(pkg)
+    set_build_environment_variables(pkg)
+    set_module_variables_for_package(pkg)
+
+    # Allow dependencies to set up environment as well.
+    for dep_spec in pkg.spec.traverse(root=False):
+        dep_spec.package.setup_dependent_environment(
+            pkg.module, dep_spec, pkg.spec)
+
+
+def fork(pkg, function):
+    """Fork a child process to do part of a spack build.
+
+    Arguments:
+
+    pkg -- pkg whose environemnt we should set up the
+           forked process for.
+    function -- arg-less function to run in the child process.
+
+    Usage:
+       def child_fun():
+           # do stuff
+       build_env.fork(pkg, child_fun)
+
+    Forked processes are run with the build environemnt set up by
+    spack.build_environment.  This allows package authors to have
+    full control over the environment, etc. without offecting
+    other builds that might be executed in the same spack call.
+
+    If something goes wrong, the child process is expected toprint
+    the error and the parent process will exit with error as
+    well. If things go well, the child exits and the parent
+    carries on.
+    """
+    try:
+        pid = os.fork()
+    except OSError, e:
+        raise InstallError("Unable to fork build process: %s" % e)
+
+    if pid == 0:
+        # Give the child process the package's build environemnt.
+        setup_package(pkg)
+
+        try:
+            # call the forked function.
+            function()
+
+            # Use os._exit here to avoid raising a SystemExit exception,
+            # which interferes with unit tests.
+            os._exit(0)
+        except:
+            # Child doesn't raise or return to main spack code.
+            # Just runs default exception handler and exits.
+            sys.excepthook(*sys.exc_info())
+            os._exit(1)
+
+    else:
+        # Parent process just waits for the child to complete.  If the
+        # child exited badly, assume it already printed an appropriate
+        # message.  Just make the parent exit with an error code.
+        pid, returncode = os.waitpid(pid, 0)
+        if returncode != 0:
+            sys.exit(1)

lib/spack/spack/cmd/__init__.py

@@ -121,3 +121,18 @@ def elide_list(line_list, max_num=10):
         return line_list[:max_num-1] + ['...'] + line_list[-1:]
     else:
         return line_list
+
+
+def disambiguate_spec(spec):
+    matching_specs = spack.db.get_installed(spec)
+    if not matching_specs:
+        tty.die("Spec '%s' matches no installed packages." % spec)
+
+    elif len(matching_specs) > 1:
+        args =  ["%s matches multiple packages." % spec,
+                 "Matching packages:"]
+        args += ["  " + str(s) for s in matching_specs]
+        args += ["Use a more specific spec."]
+        tty.die(*args)
+
+    return matching_specs[0]

lib/spack/spack/cmd/activate.py

@@ -0,0 +1,58 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from external import argparse
+import llnl.util.tty as tty
+import spack
+import spack.cmd
+
+description = "Activate a package extension."
+
+def setup_parser(subparser):
+    subparser.add_argument(
+        '-f', '--force', action='store_true',
+        help="Activate without first activating dependencies.")
+    subparser.add_argument(
+        'spec', nargs=argparse.REMAINDER, help="spec of package extension to activate.")
+
+
+def activate(parser, args):
+    # TODO: shouldn't have to concretize here.  Fix DAG issues.
+    specs = spack.cmd.parse_specs(args.spec, concretize=True)
+    if len(specs) != 1:
+        tty.die("activate requires one spec.  %d given." % len(specs))
+
+    # TODO: remove this hack when DAG info is stored in dir layout.
+    # This ensures the ext spec is always normalized properly.
+    spack.db.get(specs[0])
+
+    spec = spack.cmd.disambiguate_spec(specs[0])
+
+    if not spec.package.is_extension:
+        tty.die("%s is not an extension." % spec.name)
+
+    if spec.package.activated:
+        tty.die("Package %s is already activated." % specs[0].short_spec)
+
+    spec.package.do_activate()

lib/spack/spack/cmd/checksum.py

@@ -38,7 +38,7 @@
 from spack.stage import Stage, FailedDownloadError
 from spack.version import *
 
-description ="Checksum available versions of a package to update a package file."
+description ="Checksum available versions of a package."
 
 def setup_parser(subparser):
     subparser.add_argument(
@@ -56,7 +56,6 @@ def get_checksums(versions, urls, **kwargs):
     first_stage_function = kwargs.get('first_stage_function', None)
     keep_stage = kwargs.get('keep_stage', False)
 
-
     tty.msg("Downloading...")
     hashes = []
     for i, (url, version) in enumerate(zip(urls, versions)):
@@ -85,24 +84,24 @@ def checksum(parser, args):
     pkg = spack.db.get(args.package)
 
     # If the user asked for specific versions, use those.
-    versions = [ver(v) for v in args.versions]
-
-    if not all(type(v) == Version for v in versions):
-        tty.die("Cannot generate checksums for version lists or " +
-                "version ranges.  Use unambiguous versions.")
-
-    if not versions:
-        versions = pkg.fetch_available_versions()
+    if args.versions:
+        versions = {}
+        for v in args.versions:
+            v = ver(v)
+            if not isinstance(v, Version):
+                tty.die("Cannot generate checksums for version lists or " +
+                        "version ranges.  Use unambiguous versions.")
+            versions[v] = pkg.url_for_version(v)
+    else:
+        versions = pkg.fetch_remote_versions()
         if not versions:
-            tty.die("Could not fetch any available versions for %s." % pkg.name)
+            tty.die("Could not fetch any versions for %s." % pkg.name)
 
-    versions = list(reversed(sorted(versions)))
-    urls = [pkg.url_for_version(v) for v in versions]
+    sorted_versions = sorted(versions, reverse=True)
 
-
-    tty.msg("Found %s versions of %s." % (len(urls), pkg.name),
+    tty.msg("Found %s versions of %s." % (len(versions), pkg.name),
             *spack.cmd.elide_list(
-            ["%-10s%s" % (v,u) for v, u in zip(versions, urls)]))
+            ["%-10s%s" % (v, versions[v]) for v in sorted_versions]))
     print
     archives_to_fetch = tty.get_number(
         "How many would you like to checksum?", default=5, abort='q')
@@ -112,10 +111,12 @@ def checksum(parser, args):
         return
 
     version_hashes = get_checksums(
-        versions[:archives_to_fetch], urls[:archives_to_fetch], keep_stage=args.keep_stage)
+        sorted_versions[:archives_to_fetch],
+        [versions[v] for v in sorted_versions[:archives_to_fetch]],
+        keep_stage=args.keep_stage)
 
     if not version_hashes:
-        tty.die("Could not fetch any available versions for %s." % pkg.name)
+        tty.die("Could not fetch any versions for %s." % pkg.name)
 
     version_lines = ["    version('%s', '%s')" % (v, h) for v, h in version_hashes]
     tty.msg("Checksummed new versions of %s:" % pkg.name, *version_lines)

lib/spack/spack/cmd/clean.py

@@ -1,5 +1,5 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2014, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
@@ -28,39 +28,19 @@
 
 import spack
 import spack.cmd
-import spack.stage as stage
 
-description = "Remove staged files for packages"
+description = "Remove build stage and source tarball for packages."
 
 def setup_parser(subparser):
-    subparser.add_argument('-c', "--clean", action="store_true", dest='clean',
-                           help="run make clean in the build directory (default)")
-    subparser.add_argument('-w', "--work", action="store_true", dest='work',
-                           help="delete the build directory and re-expand it from its archive.")
-    subparser.add_argument('-d', "--dist", action="store_true", dest='dist',
-                           help="delete the downloaded archive.")
     subparser.add_argument('packages', nargs=argparse.REMAINDER,
                            help="specs of packages to clean")
 
 
 def clean(parser, args):
     if not args.packages:
-        tty.die("spack clean requires at least one package argument")
+        tty.die("spack clean requires at least one package spec.")
 
     specs = spack.cmd.parse_specs(args.packages, concretize=True)
     for spec in specs:
         package = spack.db.get(spec)
-        if args.dist:
-            package.do_clean_dist()
-            tty.msg("Cleaned %s" % package.name)
-
-        elif args.work:
-            package.do_clean_work()
-            tty.msg("Restaged %s" % package.name)
-
-        else:
-            try:
-                package.do_clean()
-            except subprocess.CalledProcessError, e:
-                tty.warn("Warning: 'make clean' didn't work.  Consider 'spack clean --work'.")
-                tty.msg("Made clean for %s" % package.name)
+        package.do_clean()

lib/spack/spack/cmd/compiler.py

@@ -25,13 +25,14 @@
 from external import argparse
 
 import llnl.util.tty as tty
+from llnl.util.tty.color import colorize
 from llnl.util.tty.colify import colify
 from llnl.util.lang import index_by
 
 import spack.compilers
 import spack.spec
 import spack.config
-from spack.compilation import get_path
+from spack.util.environment import get_path
 from spack.spec import CompilerSpec
 
 description = "Manage compilers"
@@ -96,9 +97,12 @@ def compiler_info(args):
 def compiler_list(args):
     tty.msg("Available compilers")
     index = index_by(spack.compilers.all_compilers(), 'name')
-    for name, compilers in index.items():
-        tty.hline(name, char='-', color=spack.spec.compiler_color)
-        colify(reversed(sorted(compilers)), indent=4)
+    for i, (name, compilers) in enumerate(index.items()):
+        if i >= 1: print
+
+        cname = "%s{%s}" % (spack.spec.compiler_color, name)
+        tty.hline(colorize(cname), char='-')
+        colify(reversed(sorted(compilers)))
 
 
 def compiler(parser, args):

lib/spack/spack/cmd/create.py

@@ -28,6 +28,7 @@
 import re
 from contextlib import closing
 
+from external.ordereddict import OrderedDict
 import llnl.util.tty as tty
 from llnl.util.filesystem import mkdirp
 
@@ -159,32 +160,33 @@ def create(parser, args):
     else:
         mkdirp(os.path.dirname(pkg_path))
 
-    versions = list(reversed(spack.package.find_versions_of_archive(url)))
+    versions = spack.package.find_versions_of_archive(url)
+    rkeys = sorted(versions.keys(), reverse=True)
+    versions = OrderedDict(zip(rkeys, (versions[v] for v in rkeys)))
 
     archives_to_fetch = 1
     if not versions:
         # If the fetch failed for some reason, revert to what the user provided
-        versions = [version]
-        urls = [url]
-    else:
-        urls = [spack.url.substitute_version(url, v) for v in versions]
-        if len(urls) > 1:
-            tty.msg("Found %s versions of %s:" % (len(urls), name),
-                    *spack.cmd.elide_list(
-                    ["%-10s%s" % (v,u) for v, u in zip(versions, urls)]))
-            print
-            archives_to_fetch = tty.get_number(
-                "Include how many checksums in the package file?",
-                default=5, abort='q')
+        versions = { version : url }
+    elif len(versions) > 1:
+        tty.msg("Found %s versions of %s:" % (len(versions), name),
+                *spack.cmd.elide_list(
+                    ["%-10s%s" % (v,u) for v, u in versions.iteritems()]))
+        print
+        archives_to_fetch = tty.get_number(
+            "Include how many checksums in the package file?",
+            default=5, abort='q')
 
-            if not archives_to_fetch:
-                tty.msg("Aborted.")
-                return
+        if not archives_to_fetch:
+            tty.msg("Aborted.")
+            return
 
     guesser = ConfigureGuesser()
     ver_hash_tuples = spack.cmd.checksum.get_checksums(
-        versions[:archives_to_fetch], urls[:archives_to_fetch],
-        first_stage_function=guesser, keep_stage=args.keep_stage)
+        versions.keys()[:archives_to_fetch],
+        [versions[v] for v in versions.keys()[:archives_to_fetch]],
+        first_stage_function=guesser,
+        keep_stage=args.keep_stage)
 
     if not ver_hash_tuples:
         tty.die("Could not fetch any tarballs for %s." % name)

lib/spack/spack/cmd/deactivate.py

@@ -0,0 +1,104 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from external import argparse
+import llnl.util.tty as tty
+
+import spack
+import spack.cmd
+from spack.graph import topological_sort
+
+description = "Deactivate a package extension."
+
+def setup_parser(subparser):
+    subparser.add_argument(
+        '-f', '--force', action='store_true',
+        help="Run deactivation even if spec is NOT currently activated.")
+    subparser.add_argument(
+        '-a', '--all', action='store_true',
+        help="Deactivate all extensions of an extendable pacakge, or "
+        "deactivate an extension AND its dependencies.")
+    subparser.add_argument(
+        'spec', nargs=argparse.REMAINDER, help="spec of package extension to deactivate.")
+
+
+def deactivate(parser, args):
+    # TODO: shouldn't have to concretize here.  Fix DAG issues.
+    specs = spack.cmd.parse_specs(args.spec, concretize=True)
+    if len(specs) != 1:
+        tty.die("deactivate requires one spec.  %d given." % len(specs))
+
+    # TODO: remove this hack when DAG info is stored properly.
+    # This ensures the ext spec is always normalized properly.
+    spack.db.get(specs[0])
+
+    spec = spack.cmd.disambiguate_spec(specs[0])
+    pkg = spec.package
+
+    if args.all:
+        if pkg.extendable:
+            tty.msg("Deactivating all extensions of %s" % pkg.spec.short_spec)
+            ext_pkgs = spack.db.installed_extensions_for(spec)
+
+            for ext_pkg in ext_pkgs:
+                ext_pkg.spec.normalize()
+                if ext_pkg.activated:
+                    ext_pkg.do_deactivate(force=True)
+
+        elif pkg.is_extension:
+            # TODO: store DAG info properly (see above)
+            spec.normalize()
+
+            if not args.force and not spec.package.activated:
+                tty.die("%s is not activated." % pkg.spec.short_spec)
+
+            tty.msg("Deactivating %s and all dependencies." % pkg.spec.short_spec)
+
+            topo_order = topological_sort(spec)
+            index = spec.index()
+
+            for name in topo_order:
+                espec = index[name]
+                epkg = espec.package
+
+                # TODO: store DAG info properly (see above)
+                epkg.spec.normalize()
+
+                if epkg.extends(pkg.extendee_spec):
+                    if epkg.activated or args.force:
+
+                        epkg.do_deactivate(force=args.force)
+
+        else:
+            tty.die("spack deactivate --all requires an extendable package or an extension.")
+
+    else:
+        if not pkg.is_extension:
+            tty.die("spack deactivate requires an extension.",
+                    "Did you mean 'spack deactivate --all'?")
+
+        if not args.force and not spec.package.activated:
+            tty.die("Package %s is not activated." % specs[0].short_spec)
+
+        spec.package.do_deactivate(force=args.force)

lib/spack/spack/cmd/diy.py

@@ -0,0 +1,93 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import sys
+import os
+from external import argparse
+
+import llnl.util.tty as tty
+
+import spack
+import spack.cmd
+from spack.cmd.edit import edit_package
+from spack.stage import DIYStage
+
+description = "Do-It-Yourself: build from an existing source directory."
+
+def setup_parser(subparser):
+    subparser.add_argument(
+        '-i', '--ignore-dependencies', action='store_true', dest='ignore_deps',
+        help="Do not try to install dependencies of requested packages.")
+    subparser.add_argument(
+        '--keep-prefix', action='store_true',
+        help="Don't remove the install prefix if installation fails.")
+    subparser.add_argument(
+        '--skip-patch', action='store_true',
+        help="Skip patching for the DIY build.")
+    subparser.add_argument(
+        'spec', nargs=argparse.REMAINDER,
+        help="specs to use for install.  Must contain package AND verison.")
+
+
+def diy(self, args):
+    if not args.spec:
+        tty.die("spack diy requires a package spec argument.")
+
+    specs = spack.cmd.parse_specs(args.spec)
+    if len(specs) > 1:
+        tty.die("spack diy only takes one spec.")
+
+    spec = specs[0]
+    if not spack.db.exists(spec.name):
+        tty.warn("No such package: %s" % spec.name)
+        create = tty.get_yes_or_no("Create this package?", default=False)
+        if not create:
+            tty.msg("Exiting without creating.")
+            sys.exit(1)
+        else:
+            tty.msg("Running 'spack edit -f %s'" % spec.name)
+            edit_package(spec.name, True)
+            return
+
+    if not spec.version.concrete:
+        tty.die("spack diy spec must have a single, concrete version.")
+
+    spec.concretize()
+    package = spack.db.get(spec)
+
+    if package.installed:
+        tty.error("Already installed in %s" % package.prefix)
+        tty.msg("Uninstall or try adding a version suffix for this DIY build.")
+        sys.exit(1)
+
+    # Forces the build to run out of the current directory.
+    package.stage = DIYStage(os.getcwd())
+
+    # TODO: make this an argument, not a global.
+    spack.do_checksum = False
+
+    package.do_install(
+        keep_prefix=args.keep_prefix,
+        ignore_deps=args.ignore_deps,
+        keep_stage=True)   # don't remove source dir for DIY.

lib/spack/spack/cmd/edit.py

@@ -24,7 +24,6 @@
 ##############################################################################
 import os
 import string
-from contextlib import closing
 
 import llnl.util.tty as tty
 from llnl.util.filesystem import mkdirp, join_path
@@ -54,6 +53,27 @@ def install(self, spec, prefix):
 """)
 
 
+def edit_package(name, force=False):
+    path = spack.db.filename_for_package_name(name)
+
+    if os.path.exists(path):
+        if not os.path.isfile(path):
+            tty.die("Something's wrong.  '%s' is not a file!" % path)
+        if not os.access(path, os.R_OK|os.W_OK):
+            tty.die("Insufficient permissions on '%s'!" % path)
+    elif not force:
+        tty.die("No package '%s'.  Use spack create, or supply -f/--force "
+                "to edit a new file." % name)
+    else:
+        mkdirp(os.path.dirname(path))
+        with open(path, "w") as pkg_file:
+            pkg_file.write(
+                package_template.substitute(
+                    name=name, class_name=mod_to_class(name)))
+
+    spack.editor(path)
+
+
 def setup_parser(subparser):
     subparser.add_argument(
         '-f', '--force', dest='force', action='store_true',
@@ -80,22 +100,7 @@ def edit(parser, args):
         # By default open the directory where packages or commands live.
         if not name:
             path = spack.packages_path
+            spack.editor(path)
         else:
-            path = spack.db.filename_for_package_name(name)
+            edit_package(name, args.force)
 
-            if os.path.exists(path):
-                if not os.path.isfile(path):
-                    tty.die("Something's wrong.  '%s' is not a file!" % path)
-                if not os.access(path, os.R_OK|os.W_OK):
-                    tty.die("Insufficient permissions on '%s'!" % path)
-            elif not args.force:
-                tty.die("No package '%s'.  Use spack create, or supply -f/--force "
-                        "to edit a new file." % name)
-            else:
-                mkdirp(os.path.dirname(path))
-                with closing(open(path, "w")) as pkg_file:
-                    pkg_file.write(
-                        package_template.substitute(name=name, class_name=mod_to_class(name)))
-
-    # If everything checks out, go ahead and edit.
-    spack.editor(path)

lib/spack/spack/cmd/env.py

@@ -0,0 +1,69 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import os
+from external import argparse
+import llnl.util.tty as tty
+import spack.cmd
+import spack.build_environment as build_env
+
+description = "Run a command with the environment for a particular spec's install."
+
+def setup_parser(subparser):
+    subparser.add_argument(
+        'spec', nargs=argparse.REMAINDER, help="specs of package environment to emulate.")
+
+
+def env(parser, args):
+    if not args.spec:
+        tty.die("spack env requires a spec.")
+
+    # Specs may have spaces in them, so if they do, require that the
+    # caller put a '--' between the spec and the command to be
+    # executed.  If there is no '--', assume that the spec is the
+    # first argument.
+    sep = '--'
+    if sep in args.spec:
+        s = args.spec.index(sep)
+        spec = args.spec[:s]
+        cmd  = args.spec[s+1:]
+    else:
+        spec = args.spec[0]
+        cmd  = args.spec[1:]
+
+    specs = spack.cmd.parse_specs(spec, concretize=True)
+    if len(specs) > 1:
+        tty.die("spack env only takes one spec.")
+    spec = specs[0]
+
+    build_env.setup_package(spec.package)
+
+    if not cmd:
+        # If no command act like the "env" command and print out env vars.
+        for key, val in os.environ.items():
+            print "%s=%s" % (key, val)
+
+    else:
+        # Otherwise execute the command with the new environment
+        os.execvp(cmd[0], cmd)

lib/spack/spack/cmd/extensions.py

@@ -0,0 +1,98 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import sys
+from external import argparse
+
+import llnl.util.tty as tty
+from llnl.util.tty.colify import colify
+
+import spack
+import spack.cmd
+import spack.cmd.find
+
+description = "List extensions for package."
+
+def setup_parser(subparser):
+    format_group = subparser.add_mutually_exclusive_group()
+    format_group.add_argument(
+        '-l', '--long', action='store_const', dest='mode', const='long',
+        help='Show dependency hashes as well as versions.')
+    format_group.add_argument(
+        '-p', '--paths', action='store_const', dest='mode', const='paths',
+        help='Show paths to extension install directories')
+    format_group.add_argument(
+        '-d', '--deps', action='store_const', dest='mode', const='deps',
+        help='Show full dependency DAG of extensions')
+
+    subparser.add_argument(
+        'spec', nargs=argparse.REMAINDER, help='Spec of package to list extensions for')
+
+
+def extensions(parser, args):
+    if not args.spec:
+        tty.die("extensions requires a package spec.")
+
+    # Checks
+    spec = spack.cmd.parse_specs(args.spec)
+    if len(spec) > 1:
+        tty.die("Can only list extensions for one package.")
+
+    if not spec[0].package.extendable:
+        tty.die("%s is not an extendable package." % spec[0].name)
+
+    spec = spack.cmd.disambiguate_spec(spec[0])
+
+    if not spec.package.extendable:
+        tty.die("%s does not have extensions." % spec.short_spec)
+
+    if not args.mode:
+        args.mode = 'short'
+
+    # List package names of extensions
+    extensions = spack.db.extensions_for(spec)
+    if not extensions:
+        tty.msg("%s has no extensions." % spec.cshort_spec)
+        return
+    tty.msg(spec.cshort_spec)
+    tty.msg("%d extensions:" % len(extensions))
+    colify(ext.name for ext in extensions)
+
+    # List specs of installed extensions.
+    installed  = [s.spec for s in spack.db.installed_extensions_for(spec)]
+    print
+    if not installed:
+        tty.msg("None installed.")
+        return
+    tty.msg("%d installed:" % len(installed))
+    spack.cmd.find.display_specs(installed, mode=args.mode)
+
+    # List specs of activated extensions.
+    activated = spack.install_layout.extension_map(spec)
+    print
+    if not activated:
+        tty.msg("None activated.")
+        return
+    tty.msg("%d currently activated:" % len(activated))
+    spack.cmd.find.display_specs(activated.values(), mode=args.mode)

lib/spack/spack/cmd/find.py

@@ -24,13 +24,14 @@
 ##############################################################################
 import sys
 import collections
+import itertools
 from external import argparse
 from StringIO import StringIO
 
 import llnl.util.tty as tty
-from llnl.util.tty.colify import colify
+from llnl.util.tty.colify import *
 from llnl.util.tty.color import *
-from llnl.util.lang import partition_list, index_by
+from llnl.util.lang import *
 
 import spack
 import spack.spec
@@ -40,17 +41,64 @@
 def setup_parser(subparser):
     format_group = subparser.add_mutually_exclusive_group()
     format_group.add_argument(
-        '-p', '--paths', action='store_true', dest='paths',
+        '-l', '--long', action='store_const', dest='mode', const='long',
+        help='Show dependency hashes as well as versions.')
+    format_group.add_argument(
+        '-p', '--paths', action='store_const', dest='mode', const='paths',
         help='Show paths to package install directories')
     format_group.add_argument(
-        '-l', '--long', action='store_true', dest='full_specs',
-        help='Show full-length specs of installed packages')
+        '-d', '--deps', action='store_const', dest='mode', const='deps',
+        help='Show full dependency DAG of installed packages')
 
     subparser.add_argument(
         'query_specs', nargs=argparse.REMAINDER,
         help='optional specs to filter results')
 
 
+def display_specs(specs, **kwargs):
+    mode = kwargs.get('mode', 'short')
+
+    # Make a dict with specs keyed by architecture and compiler.
+    index = index_by(specs, ('architecture', 'compiler'))
+
+    # Traverse the index and print out each package
+    for i, (architecture, compiler) in enumerate(sorted(index)):
+        if i > 0: print
+
+        header = "%s{%s} / %s{%s}" % (
+            spack.spec.architecture_color, architecture,
+            spack.spec.compiler_color, compiler)
+        tty.hline(colorize(header), char='-')
+
+        specs = index[(architecture,compiler)]
+        specs.sort()
+
+        abbreviated = [s.format('$_$@$+', color=True) for s in specs]
+        if mode == 'paths':
+            # Print one spec per line along with prefix path
+            width = max(len(s) for s in abbreviated)
+            width += 2
+            format = "    %-{}s%s".format(width)
+
+            for abbrv, spec in zip(abbreviated, specs):
+                print format % (abbrv, spec.prefix)
+
+        elif mode == 'deps':
+            for spec in specs:
+                print spec.tree(indent=4, format='$_$@$+$#', color=True),
+
+        elif mode in ('short', 'long'):
+            fmt = '$-_$@$+'
+            if mode == 'long':
+                fmt += '$#'
+            colify(s.format(fmt, color=True) for s in specs)
+
+        else:
+            raise ValueError(
+                "Invalid mode for display_specs: %s. Must be one of (paths, deps, short)." % mode)
+
+
+
 def find(parser, args):
     # Filter out specs that don't exist.
     query_specs = spack.cmd.parse_specs(args.query_specs)
@@ -65,39 +113,17 @@ def find(parser, args):
         if not query_specs:
             return
 
-    specs = [s for s in spack.db.installed_package_specs()
-             if not query_specs or any(s.satisfies(q) for q in query_specs)]
+    # Get all the specs the user asked for
+    if not query_specs:
+        specs = set(spack.db.installed_package_specs())
+    else:
+        results = [set(spack.db.get_installed(qs)) for qs in query_specs]
+        specs = set.union(*results)
 
-    # Make a dict with specs keyed by architecture and compiler.
-    index = index_by(specs, 'architecture', 'compiler')
+    if not args.mode:
+        args.mode = 'short'
 
-    # Traverse the index and print out each package
-    for architecture in index:
-        tty.hline(architecture, char='=', color=spack.spec.architecture_color)
-        for compiler in index[architecture]:
-            tty.hline(compiler, char='-', color=spack.spec.compiler_color)
+    if sys.stdout.isatty():
+        tty.msg("%d installed packages." % len(specs))
+    display_specs(specs, mode=args.mode)
 
-            specs = index[architecture][compiler]
-            specs.sort()
-
-            abbreviated = [s.format('$_$@$+$#', color=True) for s in specs]
-
-            if args.paths:
-                # Print one spec per line along with prefix path
-                width = max(len(s) for s in abbreviated)
-                width += 2
-                format = "    %-{}s%s".format(width)
-
-                for abbrv, spec in zip(abbreviated, specs):
-                    print format % (abbrv, spec.prefix)
-
-            elif args.full_specs:
-                for spec in specs:
-                    print spec.tree(indent=4, format='$_$@$+', color=True),
-            else:
-                max_len = max([len(s.name) for s in specs])
-                max_len += 4
-
-                for spec in specs:
-                    format = '$-' + str(max_len) + '_$@$+$#'
-                    print "   " + spec.format(format, color=True)

lib/spack/spack/cmd/graph.py

@@ -22,9 +22,45 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import spack
+from external import argparse
+
+import spack
+import spack.cmd
+from spack.graph import *
+
+description = "Generate graphs of package dependency relationships."
+
+def setup_parser(subparser):
+    setup_parser.parser = subparser
+
+    method = subparser.add_mutually_exclusive_group()
+    method.add_argument(
+        '--ascii', action='store_true',
+        help="Draw graph as ascii to stdout (default).")
+    method.add_argument(
+        '--dot', action='store_true',
+        help="Generate graph in dot format and print to stdout.")
+
+    subparser.add_argument(
+        '--concretize', action='store_true', help="Concretize specs before graphing.")
+
+    subparser.add_argument(
+        'specs', nargs=argparse.REMAINDER, help="specs of packages to graph.")
 
-description = "Write out inter-package dependencies in dot graph format"
 
 def graph(parser, args):
-    spack.db.graph_dependencies()
+    specs = spack.cmd.parse_specs(
+        args.specs, normalize=True, concretize=args.concretize)
+
+    if not specs:
+        setup_parser.parser.print_help()
+        return 1
+
+    if args.dot:    # Dot graph only if asked for.
+        graph_dot(*specs)
+
+    elif specs:     # ascii is default: user doesn't need to provide it explicitly
+        graph_ascii(specs[0], debug=spack.debug)
+        for spec in specs[1:]:
+            print # extra line bt/w independent graphs
+            graph_ascii(spec, debug=spack.debug)

lib/spack/spack/cmd/info.py

@@ -22,94 +22,18 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import re
-import textwrap
-from StringIO import StringIO
 from llnl.util.tty.colify import *
 import spack
 import spack.fetch_strategy as fs
 
 description = "Get detailed information on a particular package"
 
+
 def setup_parser(subparser):
-    subparser.add_argument('-r', '--rst', action='store_true',
-                           help="List all packages in reStructured text, for docs.")
-    subparser.add_argument('name', metavar="PACKAGE", nargs='?', help="name of packages to get info on")
+    subparser.add_argument('name', metavar="PACKAGE", help="Name of package to get info for.")
 
 
-def format_doc(pkg, **kwargs):
-    """Wrap doc string at 72 characters and format nicely"""
-    indent = kwargs.get('indent', 0)
-
-    if not pkg.__doc__:
-        return ""
-
-    doc = re.sub(r'\s+', ' ', pkg.__doc__)
-    lines = textwrap.wrap(doc, 72)
-    results = StringIO()
-    for line in lines:
-        results.write((" " * indent) + line + "\n")
-    return results.getvalue()
-
-
-def github_url(pkg):
-    """Link to a package file on github."""
-    return ("https://github.com/scalability-llnl/spack/blob/master/var/spack/packages/%s/package.py" %
-            pkg.name)
-
-
-def rst_table(elts):
-    """Print out a RST-style table."""
-    cols = StringIO()
-    ncol, widths = colify(elts, output=cols, tty=True)
-    header = " ".join("=" * (w-1) for w in widths)
-    return "%s\n%s%s" % (header, cols.getvalue(), header)
-
-
-def info_rst():
-    """Print out information on all packages in restructured text."""
-    pkgs = sorted(spack.db.all_packages(), key=lambda s:s.name.lower())
-
-    print "Package List"
-    print "=================="
-
-    print "This is a list of things you can install using Spack.  It is"
-    print "automatically generated based on the packages in the latest Spack"
-    print "release."
-    print
-
-    print "Spack currently has %d mainline packages:" % len(pkgs)
-    print
-    print rst_table("`%s`_" % p.name for p in pkgs)
-    print
-    print "-----"
-
-    # Output some text for each package.
-    for pkg in pkgs:
-        print
-        print ".. _%s:" % pkg.name
-        print
-        print pkg.name
-        print "-" * len(pkg.name)
-        print "Links"
-        print "    * `Homepage <%s>`__" % pkg.homepage
-        print "    * `%s/package.py <%s>`__" % (pkg.name, github_url(pkg))
-        print
-        if pkg.versions:
-            print "Versions:"
-            print "  " + ", ".join(str(v) for v in reversed(sorted(pkg.versions)))
-        if pkg.dependencies:
-            print "Dependencies"
-            print "  " + ", ".join("`%s`_" % d if d != "mpi" else d
-                                   for d in pkg.dependencies)
-            print
-        print "Description"
-        print format_doc(pkg, indent=2)
-        print
-        print "-----"
-
-
-def info_text(pkg):
+def print_text_info(pkg):
     """Print out a plain text description of a package."""
     print "Package:   ", pkg.name
     print "Homepage:  ", pkg.homepage
@@ -144,17 +68,11 @@ def info_text(pkg):
     print
     print "Description:"
     if pkg.__doc__:
-        print format_doc(pkg, indent=4)
+        print pkg.format_doc(indent=4)
     else:
         print "    None"
 
 
 def info(parser, args):
-     if args.rst:
-         info_rst()
-
-     else:
-         if not args.name:
-             tty.die("You must supply a package name.")
-         pkg = spack.db.get(args.name)
-         info_text(pkg)
+    pkg = spack.db.get(args.name)
+    print_text_info(pkg)

lib/spack/spack/cmd/install.py

@@ -22,9 +22,10 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import sys
 from external import argparse
 
+import llnl.util.tty as tty
+
 import spack
 import spack.cmd
 
@@ -34,6 +35,9 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-i', '--ignore-dependencies', action='store_true', dest='ignore_deps',
         help="Do not try to install dependencies of requested packages.")
+    subparser.add_argument(
+        '-j', '--jobs', action='store', type=int,
+        help="Explicitly set number of make jobs.  Default is #cpus.")
     subparser.add_argument(
         '--keep-prefix', action='store_true', dest='keep_prefix',
         help="Don't remove the install prefix if installation fails.")
@@ -43,6 +47,9 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-n', '--no-checksum', action='store_true', dest='no_checksum',
         help="Do not check packages against checksum")
+    subparser.add_argument(
+        '--fake', action='store_true', dest='fake',
+        help="Fake install.  Just remove the prefix and touch a fake file in it.")
     subparser.add_argument(
         'packages', nargs=argparse.REMAINDER, help="specs of packages to install")
 
@@ -51,12 +58,19 @@ def install(parser, args):
     if not args.packages:
         tty.die("install requires at least one package argument")
 
+    if args.jobs is not None:
+        if args.jobs <= 0:
+            tty.die("The -j option must be a positive integer!")
+
     if args.no_checksum:
-        spack.do_checksum = False
+        spack.do_checksum = False        # TODO: remove this global.
 
     specs = spack.cmd.parse_specs(args.packages, concretize=True)
     for spec in specs:
         package = spack.db.get(spec)
-        package.do_install(keep_prefix=args.keep_prefix,
-                           keep_stage=args.keep_stage,
-                           ignore_deps=args.ignore_deps)
+        package.do_install(
+            keep_prefix=args.keep_prefix,
+            keep_stage=args.keep_stage,
+            ignore_deps=args.ignore_deps,
+            make_jobs=args.jobs,
+            fake=args.fake)

lib/spack/spack/cmd/list.py

@@ -61,5 +61,4 @@ def match(p, f):
     indent=0
     if sys.stdout.isatty():
         tty.msg("%d packages." % len(sorted_packages))
-        indent=2
     colify(sorted_packages, indent=indent)

lib/spack/spack/cmd/location.py

@@ -23,6 +23,7 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
+import sys
 from external import argparse
 
 import llnl.util.tty as tty
@@ -77,38 +78,30 @@ def location(parser, args):
             tty.die("You must supply a spec.")
         if len(specs) != 1:
             tty.die("Too many specs.  Supply only one.")
-        spec = specs[0]
 
         if args.install_dir:
             # install_dir command matches against installed specs.
-            matching_specs = spack.db.get_installed(spec)
-            if not matching_specs:
-                tty.die("Spec '%s' matches no installed packages." % spec)
-
-            elif len(matching_specs) > 1:
-                args =  ["%s matches multiple packages." % spec,
-                         "Matching packages:"]
-                args += ["  " + str(s) for s in matching_specs]
-                args += ["Use a more specific spec."]
-                tty.die(*args)
-
-            print matching_specs[0].prefix
-
-        elif args.package_dir:
-            # This one just needs the spec name.
-            print join_path(spack.db.root, spec.name)
+            spec = spack.cmd.disambiguate_spec(specs[0])
+            print spec.prefix
 
         else:
-            # These versions need concretized specs.
-            spec.concretize()
-            pkg = spack.db.get(spec)
+            spec = specs[0]
 
-            if args.stage_dir:
-                print pkg.stage.path
+            if args.package_dir:
+                # This one just needs the spec name.
+                print join_path(spack.db.root, spec.name)
 
-            else:  #  args.build_dir is the default.
-                if not pkg.stage.source_path:
-                    tty.die("Build directory does not exist yet. Run this to create it:",
-                            "spack stage " + " ".join(args.spec))
-                print pkg.stage.source_path
+            else:
+                # These versions need concretized specs.
+                spec.concretize()
+                pkg = spack.db.get(spec)
+
+                if args.stage_dir:
+                    print pkg.stage.path
+
+                else:  #  args.build_dir is the default.
+                    if not pkg.stage.source_path:
+                        tty.die("Build directory does not exist yet. Run this to create it:",
+                                "spack stage " + " ".join(args.spec))
+                    print pkg.stage.source_path
 

lib/spack/spack/cmd/md5.py

@@ -41,6 +41,7 @@ def setup_parser(subparser):
 def md5(parser, args):
     if not args.files:
         setup_parser.parser.print_help()
+        return 1
 
     for f in args.files:
         if not os.path.isfile(f):

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

@@ -0,0 +1,95 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import re
+import cgi
+from StringIO import StringIO
+import llnl.util.tty as tty
+from llnl.util.tty.colify import *
+import spack
+
+description = "Print a list of all packages in reStructuredText."
+
+
+def github_url(pkg):
+    """Link to a package file on github."""
+    return ("https://github.com/scalability-llnl/spack/blob/master/var/spack/packages/%s/package.py" %
+            pkg.name)
+
+
+def rst_table(elts):
+    """Print out a RST-style table."""
+    cols = StringIO()
+    ncol, widths = colify(elts, output=cols, tty=True)
+    header = " ".join("=" * (w-1) for w in widths)
+    return "%s\n%s%s" % (header, cols.getvalue(), header)
+
+
+def print_rst_package_list():
+    """Print out information on all packages in restructured text."""
+    pkgs = sorted(spack.db.all_packages(), key=lambda s:s.name.lower())
+
+    print ".. _package-list:"
+    print
+    print "Package List"
+    print "=================="
+
+    print "This is a list of things you can install using Spack.  It is"
+    print "automatically generated based on the packages in the latest Spack"
+    print "release."
+    print
+
+    print "Spack currently has %d mainline packages:" % len(pkgs)
+    print
+    print rst_table("`%s`_" % p.name for p in pkgs)
+    print
+    print "-----"
+
+    # Output some text for each package.
+    for pkg in pkgs:
+        print
+        print ".. _%s:" % pkg.name
+        print
+        print pkg.name
+        print "-" * len(pkg.name)
+        print "Links:"
+        print "  * `%s <%s>`__" % (cgi.escape(pkg.homepage), pkg.homepage)
+        print "  * `%s/package.py <%s>`__" % (pkg.name, github_url(pkg))
+        print
+        if pkg.versions:
+            print "Versions:"
+            print "  " + ", ".join(str(v) for v in reversed(sorted(pkg.versions)))
+        if pkg.dependencies:
+            print "Dependencies"
+            print "  " + ", ".join("`%s`_" % d if d != "mpi" else d
+                                   for d in pkg.dependencies)
+            print
+        print "Description:"
+        print pkg.format_doc(indent=2)
+        print
+        print "-----"
+
+
+def package_list(parser, args):
+    print_rst_package_list()

lib/spack/spack/cmd/pkg.py

@@ -31,12 +31,16 @@
 import spack
 from spack.util.executable import *
 
-description = "Query packages associated with particular git revisions in spack."
+description = "Query packages associated with particular git revisions."
 
 def setup_parser(subparser):
     sp = subparser.add_subparsers(
         metavar='SUBCOMMAND', dest='pkg_command')
 
+    add_parser = sp.add_parser('add', help=pkg_add.__doc__)
+    add_parser.add_argument('packages', nargs=argparse.REMAINDER,
+                            help="Names of packages to add to git repo.")
+
     list_parser = sp.add_parser('list', help=pkg_list.__doc__)
     list_parser.add_argument('rev', default='HEAD', nargs='?',
                              help="Revision to list packages for.")
@@ -79,6 +83,16 @@ def list_packages(rev):
     return sorted(line[len(relpath):] for line in output.split('\n') if line)
 
 
+def pkg_add(args):
+    for pkg_name in args.packages:
+        filename = spack.db.filename_for_package_name(pkg_name)
+        if not os.path.isfile(filename):
+            tty.die("No such package: %s.  Path does not exist:" % pkg_name, filename)
+
+        git = get_git()
+        git('-C', spack.packages_path, 'add', filename)
+
+
 def pkg_list(args):
     """List packages associated with a particular spack git revision."""
     colify(list_packages(args.rev))
@@ -117,7 +131,8 @@ def pkg_added(args):
 
 
 def pkg(parser, args):
-    action = { 'diff'    : pkg_diff,
+    action = { 'add'    : pkg_add,
+               'diff'    : pkg_diff,
                'list'    : pkg_list,
                'removed' : pkg_removed,
                'added'   : pkg_added }

lib/spack/spack/cmd/restage.py

@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2014, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from external import argparse
+
+import llnl.util.tty as tty
+
+import spack
+import spack.cmd
+
+description = "Revert checked out package source code."
+
+def setup_parser(subparser):
+    subparser.add_argument('packages', nargs=argparse.REMAINDER,
+                           help="specs of packages to restage")
+
+
+def restage(parser, args):
+    if not args.packages:
+        tty.die("spack restage requires at least one package spec.")
+
+    specs = spack.cmd.parse_specs(args.packages, concretize=True)
+    for spec in specs:
+        package = spack.db.get(spec)
+        package.do_restage()

lib/spack/spack/cmd/spec.py

@@ -27,26 +27,33 @@
 
 import llnl.util.tty as tty
 
-import spack.url as url
 import spack
+import spack.url as url
 
 description = "print out abstract and concrete versions of a spec."
 
 def setup_parser(subparser):
+    subparser.add_argument('-i', '--ids', action='store_true',
+                           help="show numerical ids for dependencies.")
     subparser.add_argument('specs', nargs=argparse.REMAINDER, help="specs of packages")
 
+
 def spec(parser, args):
+    kwargs = { 'ids'    : args.ids,
+               'indent' : 2,
+               'color'  : True }
+
     for spec in spack.cmd.parse_specs(args.specs):
         print "Input spec"
         print "------------------------------"
-        print spec.tree(color=True, indent=2)
+        print spec.tree(**kwargs)
 
         print "Normalized"
         print "------------------------------"
         spec.normalize()
-        print spec.tree(color=True, indent=2)
+        print spec.tree(**kwargs)
 
         print "Concretized"
         print "------------------------------"
         spec.concretize()
-        print spec.tree(color=True, indent=2)
+        print spec.tree(**kwargs)

lib/spack/spack/cmd/stage.py

@@ -36,7 +36,6 @@ def setup_parser(subparser):
         '-n', '--no-checksum', action='store_true', dest='no_checksum',
         help="Do not check downloaded packages against checksum")
 
-    dir_parser = subparser.add_mutually_exclusive_group()
     subparser.add_argument(
         'specs', nargs=argparse.REMAINDER, help="specs of packages to stage")
 
@@ -52,4 +51,3 @@ def stage(parser, args):
     for spec in specs:
         package = spack.db.get(spec)
         package.do_stage()
-

lib/spack/spack/cmd/uninstall.py

@@ -65,20 +65,19 @@ def uninstall(parser, args):
                      "  b) use a more specific spec."]
             tty.die(*args)
 
-
         if len(matching_specs) == 0:
+            if args.force: continue
             tty.die("%s does not match any installed packages." % spec)
 
         for s in matching_specs:
             try:
                 # should work if package is known to spack
-                pkgs.append(spack.db.get(s))
+                pkgs.append(s.package)
 
             except spack.packages.UnknownPackageError, e:
                 # The package.py file has gone away -- but still want to uninstall.
                 spack.Package(s).do_uninstall(force=True)
 
-
     # Sort packages to be uninstalled by the number of installed dependents
     # This ensures we do things in the right order
     def num_installed_deps(pkg):

lib/spack/spack/cmd/urls.py

@@ -0,0 +1,58 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import sys
+import spack
+import spack.url
+
+description = "Inspect urls used by packages in spack."
+
+def setup_parser(subparser):
+    subparser.add_argument(
+        '-c', '--color', action='store_true',
+        help="Color the parsed version and name in the urls shown.  "
+             "Version will be cyan, name red.")
+    subparser.add_argument(
+        '-e', '--extrapolation', action='store_true',
+        help="Color the versions used for extrapolation as well."
+             "Additional versions are green, names magenta.")
+
+
+def urls(parser, args):
+    urls = set()
+    for pkg in spack.db.all_packages():
+        url = getattr(pkg.__class__, 'url', None)
+        if url:
+            urls.add(url)
+
+        for params in pkg.versions.values():
+            url = params.get('url', None)
+            if url:
+                urls.add(url)
+
+    for url in sorted(urls):
+        if args.color or args.extrapolation:
+            print spack.url.color_url(url, subs=args.extrapolation, errors=True)
+        else:
+            print url

lib/spack/spack/cmd/versions.py

@@ -24,6 +24,7 @@
 ##############################################################################
 import os
 from llnl.util.tty.colify import colify
+import llnl.util.tty as tty
 import spack
 
 description ="List available versions of a package"
@@ -34,4 +35,21 @@ def setup_parser(subparser):
 
 def versions(parser, args):
     pkg = spack.db.get(args.package)
-    colify(reversed(pkg.fetch_available_versions()))
+
+    safe_versions = pkg.versions
+    fetched_versions = pkg.fetch_remote_versions()
+    remote_versions = set(fetched_versions).difference(safe_versions)
+
+    tty.msg("Safe versions (already checksummed):")
+    colify(sorted(safe_versions, reverse=True), indent=2)
+
+    tty.msg("Remote versions (not yet checksummed):")
+    if not remote_versions:
+        if not fetched_versions:
+            print "  Found no versions for %s" % pkg.name
+            tty.debug("Check the list_url and list_depth attribute on the "
+                      "package to help Spack find versions.")
+        else:
+            print "  Found no unckecksummed versions for %s" % pkg.name
+    else:
+        colify(sorted(remote_versions, reverse=True), indent=2)

lib/spack/spack/compilation.py

@@ -1,117 +0,0 @@
-##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://scalability-llnl.github.io/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-"""\
-The ``compilation`` module contains utility functions used by the compiler
-wrapper script.
-
-.. todo::
-
-   Think about moving this into the script to increase compilation
-   speed.
-
-"""
-import os
-import sys
-
-
-def get_env_var(name, required=True):
-    value = os.environ.get(name)
-    if required and value is None:
-        print "%s must be run from spack." % os.path.abspath(sys.argv[0])
-        sys.exit(1)
-    return value
-
-
-def get_env_flag(name, required=False):
-    value = get_env_var(name, required)
-    if value:
-        return value.lower() == "true"
-    return False
-
-
-def get_path(name):
-    path = os.environ.get(name, "").strip()
-    if path:
-        return path.split(":")
-    else:
-        return []
-
-
-def parse_rpaths(arguments):
-    """argparse, for all its features, cannot understand most compilers'
-       rpath arguments.  This handles '-Wl,', '-Xlinker', and '-R'"""
-    def get_next(arg, args):
-        """Get an expected next value of an iterator, or die if it's not there"""
-        try:
-            return next(args)
-        except StopIteration:
-            # quietly ignore -rpath and -Xlinker without args.
-            return None
-
-    other_args = []
-    def linker_args():
-        """This generator function allows us to parse the linker args separately
-           from the compiler args, so that we can handle them more naturally.
-        """
-        args = iter(arguments)
-        for arg in args:
-            if arg.startswith('-Wl,'):
-                sub_args = [sub for sub in arg.replace('-Wl,', '', 1).split(',')]
-                for arg in sub_args:
-                    yield arg
-            elif arg == '-Xlinker':
-                target = get_next(arg, args)
-                if target is not None:
-                    yield target
-            else:
-                other_args.append(arg)
-
-    # Extract all the possible ways rpath can appear in linker args, then
-    # append non-rpaths to other_args.  This happens in-line as the linker
-    # args are extracted, so we preserve the original order of arguments.
-    # This is important for args like --whole-archive, --no-whole-archive,
-    # and others that tell the linker how to handle the next few libraries
-    # it encounters on the command line.
-    rpaths = []
-    largs = linker_args()
-    for arg in largs:
-        if arg == '-rpath':
-            target = get_next(arg, largs)
-            if target is not None:
-                rpaths.append(target)
-
-        elif arg.startswith('-R'):
-            target = arg.replace('-R', '', 1)
-            if not target:
-                target = get_next(arg, largs)
-                if target is None: break
-
-            if os.path.isdir(target):
-                rpaths.append(target)
-            else:
-                other_args.extend(['-Wl,' + arg, '-Wl,' + target])
-        else:
-            other_args.append('-Wl,' + arg)
-    return rpaths, other_args

lib/spack/spack/compiler.py

@@ -35,8 +35,8 @@
 import spack.spec
 from spack.util.multiproc import parmap
 from spack.util.executable import *
+from spack.util.environment import get_path
 from spack.version import Version
-from spack.compilation import get_path
 
 __all__ = ['Compiler', 'get_compiler_version']
 
@@ -169,6 +169,10 @@ def _find_matches_in_path(cls, compiler_names, detect_version, *path):
 
         checks = []
         for directory in path:
+            if not (os.path.isdir(directory) and
+                    os.access(directory, os.R_OK | os.X_OK)):
+                continue
+
             files = os.listdir(directory)
             for exe in files:
                 full_path = join_path(directory, exe)

lib/spack/spack/compilers/__init__.py

@@ -40,12 +40,12 @@
 from spack.compiler import Compiler
 from spack.util.executable import which
 from spack.util.naming import mod_to_class
-from spack.compilation import get_path
+from spack.util.environment import get_path
 
 _imported_compilers_module = 'spack.compilers'
 _required_instance_vars = ['cc', 'cxx', 'f77', 'fc']
 
-_default_order = ['gcc', 'intel', 'pgi', 'clang']
+_default_order = ['gcc', 'intel', 'pgi', 'clang', 'xlc']
 
 def _auto_compiler_spec(function):
     def converter(cspec_like):

lib/spack/spack/compilers/xl.py

@@ -0,0 +1,97 @@
+# -*- coding: utf-8 -*-
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by François Bissey, francois.bissey@canterbury.ac.nz, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack.compiler import *
+
+class Xl(Compiler):
+    # Subclasses use possible names of C compiler
+    cc_names = ['xlc','xlc_r']
+
+    # Subclasses use possible names of C++ compiler
+    cxx_names = ['xlC','xlC_r','xlc++','xlc++_r']
+
+    # Subclasses use possible names of Fortran 77 compiler
+    f77_names = ['xlf','xlf_r']
+
+    # Subclasses use possible names of Fortran 90 compiler
+    fc_names = ['xlf90','xlf90_r','xlf95','xlf95_r','xlf2003','xlf2003_r','xlf2008','xlf2008_r']
+
+    @property
+    def cxx11_flag(self):
+        if self.version < ver('13.1'):
+            tty.die("Only xlC 13.1 and above have some c++11 support.")
+        else:
+            return "-qlanglvl=extended0x"
+
+    @classmethod
+    def default_version(self, comp):
+        """The '-qversion' is the standard option fo XL compilers.
+           Output looks like this::
+
+              IBM XL C/C++ for Linux, V11.1 (5724-X14)
+              Version: 11.01.0000.0000
+
+           or::
+
+              IBM XL Fortran for Linux, V13.1 (5724-X16)
+              Version: 13.01.0000.0000
+
+           or::
+
+              IBM XL C/C++ for AIX, V11.1 (5724-X13)
+              Version: 11.01.0000.0009
+
+           or::
+
+              IBM XL C/C++ Advanced Edition for Blue Gene/P, V9.0
+              Version: 09.00.0000.0017
+        """
+
+        return get_compiler_version(
+            comp, '-qversion',r'([0-9]?[0-9]\.[0-9])')
+
+    @classmethod
+    def fc_version(cls, fc):
+        """The fortran and C/C++ versions of the XL compiler are always two units apart.
+           By this we mean that the fortran release that goes with XL C/C++ 11.1 is 13.1.
+           Having such a difference in version number is confusing spack quite a lot.
+           Most notably if you keep the versions as is the default xl compiler will only
+           have fortran and no C/C++.
+           So we associate the Fortran compiler with the version associated to the C/C++
+           compiler.
+           One last stumble. Version numbers over 10 have at least a .1 those under 10
+           a .0. There is no xlf 9.x or under currently available. BG/P and BG/L can
+           such a compiler mix and possibly older version of AIX and linux on power.
+        """
+        fver = get_compiler_version(fc, '-qversion',r'([0-9]?[0-9]\.[0-9])')
+        cver = float(fver) - 2
+        if cver < 10 :
+          cver = cver - 0.1
+        return str(cver)
+
+
+    @classmethod
+    def f77_version(cls, f77):
+        return cls.fc_version(f77)

lib/spack/spack/concretize.py

@@ -68,8 +68,9 @@ def concretize_version(self, spec):
         # If there are known avaialble versions, return the most recent
         # version that satisfies the spec
         pkg = spec.package
-        valid_versions = [v for v in pkg.available_versions
-                          if any(v.satisfies(sv) for sv in spec.versions)]
+        valid_versions = sorted(
+            [v for v in pkg.versions
+             if any(v.satisfies(sv) for sv in spec.versions)])
 
         if valid_versions:
             spec.versions = ver([valid_versions[-1]])

lib/spack/spack/directory_layout.py

@@ -27,9 +27,11 @@
 import exceptions
 import hashlib
 import shutil
+import tempfile
 from contextlib import closing
 
 import llnl.util.tty as tty
+from llnl.util.lang import memoized
 from llnl.util.filesystem import join_path, mkdirp
 
 import spack
@@ -53,6 +55,19 @@ def __init__(self, root):
         self.root = root
 
 
+    @property
+    def hidden_file_paths(self):
+        """Return a list of hidden files used by the directory layout.
+
+        Paths are relative to the root of an install directory.
+
+        If the directory layout uses no hidden files to maintain
+        state, this should return an empty container, e.g. [] or (,).
+
+        """
+        raise NotImplementedError()
+
+
     def all_specs(self):
         """To be implemented by subclasses to traverse all specs for which there is
            a directory within the root.
@@ -71,6 +86,42 @@ def make_path_for_spec(self, spec):
         raise NotImplementedError()
 
 
+    def extension_map(self, spec):
+        """Get a dict of currently installed extension packages for a spec.
+
+           Dict maps { name : extension_spec }
+           Modifying dict does not affect internals of this layout.
+        """
+        raise NotImplementedError()
+
+
+    def check_extension_conflict(self, spec, ext_spec):
+        """Ensure that ext_spec can be activated in spec.
+
+           If not, raise ExtensionAlreadyInstalledError or
+           ExtensionConflictError.
+        """
+        raise NotImplementedError()
+
+
+    def check_activated(self, spec, ext_spec):
+        """Ensure that ext_spec can be removed from spec.
+
+           If not, raise NoSuchExtensionError.
+        """
+        raise NotImplementedError()
+
+
+    def add_extension(self, spec, ext_spec):
+        """Add to the list of currently installed extensions."""
+        raise NotImplementedError()
+
+
+    def remove_extension(self, spec, ext_spec):
+        """Remove from the list of currently installed extensions."""
+        raise NotImplementedError()
+
+
     def path_for_spec(self, spec):
         """Return an absolute path from the root to a directory for the spec."""
         _check_concrete(spec)
@@ -81,12 +132,17 @@ def path_for_spec(self, spec):
 
 
     def remove_path_for_spec(self, spec):
-        """Removes a prefix and any empty parent directories from the root."""
+        """Removes a prefix and any empty parent directories from the root.
+           Raised RemoveFailedError if something goes wrong.
+        """
         path = self.path_for_spec(spec)
         assert(path.startswith(self.root))
 
         if os.path.exists(path):
-            shutil.rmtree(path, True)
+            try:
+                shutil.rmtree(path)
+            except exceptions.OSError, e:
+                raise RemoveFailedError(spec, path, e)
 
         path = os.path.dirname(path)
         while path != self.root:
@@ -134,9 +190,18 @@ def __init__(self, root, **kwargs):
         """Prefix size is number of characters in the SHA-1 prefix to use
            to make each hash unique.
         """
-        spec_file_name   = kwargs.get('spec_file_name', '.spec')
+        spec_file_name = kwargs.get('spec_file_name', '.spec')
+        extension_file_name = kwargs.get('extension_file_name', '.extensions')
         super(SpecHashDirectoryLayout, self).__init__(root)
         self.spec_file_name = spec_file_name
+        self.extension_file_name = extension_file_name
+
+        # Cache of already written/read extension maps.
+        self._extension_maps = {}
+
+    @property
+    def hidden_file_paths(self):
+        return ('.spec', '.extensions')
 
 
     def relative_path_for_spec(self, spec):
@@ -157,19 +222,27 @@ def read_spec(self, path):
             # Specs from files are assumed normal and concrete
             spec = Spec(spec_file.read().replace('\n', ''))
 
-        # If we do not have a package on hand for this spec, we know
-        # it is concrete, and we *assume* that it is normal. This
-        # prevents us from trying to fetch a non-existing package, and
-        # allows best effort for commands like spack find.
-        if not spack.db.exists(spec.name):
-            spec._normal = True
-            spec._concrete = True
-        else:
-            spec.normalize()
-            if not spec.concrete:
-                tty.warn("Spec read from installed package is not concrete:",
-                         path, spec)
+        if all(spack.db.exists(s.name) for s in spec.traverse()):
+            copy = spec.copy()
 
+            # TODO: It takes a lot of time to normalize every spec on read.
+            # TODO: Storing graph info with spec files would fix this.
+            copy.normalize()
+            if copy.concrete:
+                return copy   # These are specs spack still understands.
+
+        # If we get here, either the spec is no longer in spack, or
+        # something about its dependencies has changed. So we need to
+        # just assume the read spec is correct.  We'll lose graph
+        # information if we do this, but this is just for best effort
+        # for commands like uninstall and find.  Currently Spack
+        # doesn't do anything that needs the graph info after install.
+
+        # TODO: store specs with full connectivity information, so
+        # that we don't have to normalize or reconstruct based on
+        # changing dependencies in the Spack tree.
+        spec._normal = True
+        spec._concrete = True
         return spec
 
 
@@ -207,17 +280,116 @@ def make_path_for_spec(self, spec):
         self.write_spec(spec, spec_file_path)
 
 
+    @memoized
     def all_specs(self):
         if not os.path.isdir(self.root):
-            return
+            return []
 
+        specs = []
         for path in traverse_dirs_at_depth(self.root, 3):
             arch, compiler, last_dir = path
             spec_file_path = join_path(
                 self.root, arch, compiler, last_dir, self.spec_file_name)
             if os.path.exists(spec_file_path):
                 spec = self.read_spec(spec_file_path)
-                yield spec
+                specs.append(spec)
+        return specs
+
+
+    def extension_file_path(self, spec):
+        """Gets full path to an installed package's extension file"""
+        _check_concrete(spec)
+        return join_path(self.path_for_spec(spec), self.extension_file_name)
+
+
+    def _extension_map(self, spec):
+        """Get a dict<name -> spec> for all extensions currnetly
+           installed for this package."""
+        _check_concrete(spec)
+
+        if not spec in self._extension_maps:
+            path = self.extension_file_path(spec)
+            if not os.path.exists(path):
+                self._extension_maps[spec] = {}
+
+            else:
+                exts = {}
+                with closing(open(path)) as ext_file:
+                    for line in ext_file:
+                        try:
+                            spec = Spec(line.strip())
+                            exts[spec.name] = spec
+                        except spack.error.SpackError, e:
+                            # TODO: do something better here -- should be
+                            # resilient to corrupt files.
+                            raise InvalidExtensionSpecError(str(e))
+                self._extension_maps[spec] = exts
+
+        return self._extension_maps[spec]
+
+
+    def extension_map(self, spec):
+        """Defensive copying version of _extension_map() for external API."""
+        return self._extension_map(spec).copy()
+
+
+    def check_extension_conflict(self, spec, ext_spec):
+        exts = self._extension_map(spec)
+        if ext_spec.name in exts:
+            installed_spec = exts[ext_spec.name]
+            if ext_spec == installed_spec:
+                raise ExtensionAlreadyInstalledError(spec, ext_spec)
+            else:
+                raise ExtensionConflictError(spec, ext_spec, installed_spec)
+
+
+    def check_activated(self, spec, ext_spec):
+        exts = self._extension_map(spec)
+        if (not ext_spec.name in exts) or (ext_spec != exts[ext_spec.name]):
+            raise NoSuchExtensionError(spec, ext_spec)
+
+
+    def _write_extensions(self, spec, extensions):
+        path = self.extension_file_path(spec)
+
+        # Create a temp file in the same directory as the actual file.
+        dirname, basename = os.path.split(path)
+        tmp = tempfile.NamedTemporaryFile(
+            prefix=basename, dir=dirname, delete=False)
+
+        # Write temp file.
+        with closing(tmp):
+            for extension in sorted(extensions.values()):
+                tmp.write("%s\n" % extension)
+
+        # Atomic update by moving tmpfile on top of old one.
+        os.rename(tmp.name, path)
+
+
+    def add_extension(self, spec, ext_spec):
+        _check_concrete(spec)
+        _check_concrete(ext_spec)
+
+        # Check whether it's already installed or if it's a conflict.
+        exts = self._extension_map(spec)
+        self.check_extension_conflict(spec, ext_spec)
+
+        # do the actual adding.
+        exts[ext_spec.name] = ext_spec
+        self._write_extensions(spec, exts)
+
+
+    def remove_extension(self, spec, ext_spec):
+        _check_concrete(spec)
+        _check_concrete(ext_spec)
+
+        # Make sure it's installed before removing.
+        exts = self._extension_map(spec)
+        self.check_activated(spec, ext_spec)
+
+        # do the actual removing.
+        del exts[ext_spec.name]
+        self._write_extensions(spec, exts)
 
 
 class DirectoryLayoutError(SpackError):
@@ -234,6 +406,15 @@ def __init__(self, installed_spec, new_spec):
             % installed_spec, new_spec)
 
 
+class RemoveFailedError(DirectoryLayoutError):
+    """Raised when a DirectoryLayout cannot remove an install prefix."""
+    def __init__(self, installed_spec, prefix, error):
+        super(RemoveFailedError, self).__init__(
+            'Could not remove prefix %s for %s : %s'
+            % prefix, installed_spec.short_spec, error)
+        self.cause = error
+
+
 class InconsistentInstallDirectoryError(DirectoryLayoutError):
     """Raised when a package seems to be installed to the wrong place."""
     def __init__(self, message):
@@ -245,3 +426,34 @@ class InstallDirectoryAlreadyExistsError(DirectoryLayoutError):
     def __init__(self, path):
         super(InstallDirectoryAlreadyExistsError, self).__init__(
             "Install path %s already exists!")
+
+
+class InvalidExtensionSpecError(DirectoryLayoutError):
+    """Raised when an extension file has a bad spec in it."""
+    def __init__(self, message):
+        super(InvalidExtensionSpecError, self).__init__(message)
+
+
+class ExtensionAlreadyInstalledError(DirectoryLayoutError):
+    """Raised when an extension is added to a package that already has it."""
+    def __init__(self, spec, ext_spec):
+        super(ExtensionAlreadyInstalledError, self).__init__(
+            "%s is already installed in %s" % (ext_spec.short_spec, spec.short_spec))
+
+
+class ExtensionConflictError(DirectoryLayoutError):
+    """Raised when an extension is added to a package that already has it."""
+    def __init__(self, spec, ext_spec, conflict):
+        super(ExtensionConflictError, self).__init__(
+            "%s cannot be installed in %s because it conflicts with %s."% (
+                ext_spec.short_spec, spec.short_spec, conflict.short_spec))
+
+
+class NoSuchExtensionError(DirectoryLayoutError):
+    """Raised when an extension isn't there on deactivate."""
+    def __init__(self, spec, ext_spec):
+        super(NoSuchExtensionError, self).__init__(
+            "%s cannot be removed from %s because it's not activated."% (
+                ext_spec.short_spec, spec.short_spec))
+
+

lib/spack/spack/error.py

@@ -33,6 +33,12 @@ def __init__(self, message, long_message=None):
         self.long_message = long_message
 
 
+    def __str__(self):
+        msg = self.message
+        if self.long_message:
+            msg += "\n    %s" % self.long_message
+        return msg
+
 class UnsupportedPlatformError(SpackError):
     """Raised by packages when a platform is not supported"""
     def __init__(self, message):

lib/spack/spack/fetch_strategy.py

@@ -41,11 +41,12 @@
         Archive a source directory, e.g. for creating a mirror.
 """
 import os
+import sys
 import re
 import shutil
 from functools import wraps
 import llnl.util.tty as tty
-
+from llnl.util.filesystem import *
 import spack
 import spack.error
 import spack.util.crypto as crypto
@@ -141,13 +142,19 @@ def fetch(self):
 
         tty.msg("Trying to fetch from %s" % self.url)
 
+        curl_args = ['-O',        # save file to disk
+                     '-f',        # fail on >400 errors
+                     '-D', '-',   # print out HTML headers
+                     '-L', self.url,]
+
+        if sys.stdout.isatty():
+            curl_args.append('-#')  # status bar when using a tty
+        else:
+            curl_args.append('-sS') # just errors when not.
+
         # Run curl but grab the mime type from the http headers
-        headers = spack.curl('-#',        # status bar
-                             '-O',        # save file to disk
-                             '-f',        # fail on >400 errors
-                             '-D', '-',   # print out HTML headers
-                             '-L', self.url,
-                             return_output=True, fail_on_error=False)
+        headers = spack.curl(
+            *curl_args, return_output=True, fail_on_error=False)
 
         if spack.curl.returncode != 0:
             # clean up archive on failure.
@@ -156,9 +163,10 @@ def fetch(self):
 
             if spack.curl.returncode == 22:
                 # This is a 404.  Curl will print the error.
-                raise FailedDownloadError(url)
+                raise FailedDownloadError(
+                    self.url, "URL %s was not found!" % self.url)
 
-            if spack.curl.returncode == 60:
+            elif spack.curl.returncode == 60:
                 # This is a certificate error.  Suggest spack -k
                 raise FailedDownloadError(
                     self.url,
@@ -168,6 +176,13 @@ def fetch(self):
                     "can try running spack -k, which will not check SSL certificates."
                     "Use this at your own risk.")
 
+            else:
+                # This is some other curl error.  Curl will print the
+                # error, but print a spack message too
+                raise FailedDownloadError(
+                    self.url, "Curl failed with error %d" % spack.curl.returncode)
+
+
         # Check if we somehow got an HTML file rather than the archive we
         # asked for.  We only look at the last content type, to handle
         # redirects properly.
@@ -197,8 +212,26 @@ def expand(self):
                                       "Failed on expand() for URL %s" % self.url)
 
         decompress = decompressor_for(self.archive_file)
+
+        # Expand all tarballs in their own directory to contain
+        # exploding tarballs.
+        tarball_container = os.path.join(self.stage.path, "spack-expanded-archive")
+        mkdirp(tarball_container)
+        os.chdir(tarball_container)
         decompress(self.archive_file)
 
+        # If the tarball *didn't* explode, move
+        # the expanded directory up & remove the protector directory.
+        files = os.listdir(tarball_container)
+        if len(files) == 1:
+            expanded_dir = os.path.join(tarball_container, files[0])
+            if os.path.isdir(expanded_dir):
+                shutil.move(expanded_dir, self.stage.path)
+                os.rmdir(tarball_container)
+
+        # Set the wd back to the stage when done.
+        self.stage.chdir()
+
 
     def archive(self, destination):
         """Just moves this archive to the destination."""
@@ -330,15 +363,10 @@ def __init__(self, **kwargs):
             'git', 'tag', 'branch', 'commit', **kwargs)
         self._git = None
 
-        # For git fetch branches and tags the same way.
-        if not self.branch:
-            self.branch = self.tag
-
 
     @property
     def git_version(self):
-        git = which('git', required=True)
-        vstring = git('--version', return_output=True).lstrip('git version ')
+        vstring = self.git('--version', return_output=True).lstrip('git version ')
         return Version(vstring)
 
 
@@ -348,6 +376,7 @@ def git(self):
             self._git = which('git', required=True)
         return self._git
 
+
     @_needs_stage
     def fetch(self):
         self.stage.chdir()
@@ -389,6 +418,12 @@ def fetch(self):
             self.git(*args)
             self.stage.chdir_to_source()
 
+            # For tags, be conservative and check them out AFTER
+            # cloning.  Later git versions can do this with clone
+            # --branch, but older ones fail.
+            if self.tag:
+                self.git('checkout', self.tag)
+
 
     def archive(self, destination):
         super(GitFetchStrategy, self).archive(destination, exclude='.git')
@@ -580,7 +615,7 @@ def for_package_version(pkg, version):
        version() in the package description."""
     # If it's not a known version, extrapolate one.
     if not version in pkg.versions:
-        url = pkg.url_for_verison(version)
+        url = pkg.url_for_version(version)
         if not url:
             raise InvalidArgsError(pkg, version)
         return URLFetchStrategy(url)

lib/spack/spack/graph.py

@@ -0,0 +1,553 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+"""Functions for graphing DAGs of dependencies.
+
+This file contains code for graphing DAGs of software packages
+(i.e. Spack specs).  There are two main functions you probably care
+about:
+
+graph_ascii() will output a colored graph of a spec in ascii format,
+kind of like the graph git shows with "git log --graph", e.g.::
+
+    o  mpileaks
+    |\
+    | |\
+    | o |  callpath
+    |/| |
+    | |\|
+    | |\ \
+    | | |\ \
+    | | | | o  adept-utils
+    | |_|_|/|
+    |/| | | |
+    o | | | |  mpi
+     / / / /
+    | | o |  dyninst
+    | |/| |
+    |/|/| |
+    | | |/
+    | o |  libdwarf
+    |/ /
+    o |  libelf
+     /
+    o  boost
+
+graph_dot() will output a graph of a spec (or multiple specs) in dot
+format.
+
+Note that ``graph_ascii`` assumes a single spec while ``graph_dot``
+can take a number of specs as input.
+
+"""
+__all__ = ['topological_sort', 'graph_ascii', 'AsciiGraph', 'graph_dot']
+
+from heapq import *
+
+from llnl.util.lang import *
+from llnl.util.tty.color import *
+
+import spack
+from spack.spec import Spec
+
+
+def topological_sort(spec, **kwargs):
+    """Topological sort for specs.
+
+    Return a list of dependency specs sorted topologically.  The spec
+    argument is not modified in the process.
+
+    """
+    reverse = kwargs.get('reverse', False)
+    if not reverse:
+        parents  = lambda s: s.dependents
+        children = lambda s: s.dependencies
+    else:
+        parents  = lambda s: s.dependencies
+        children = lambda s: s.dependents
+
+    # Work on a copy so this is nondestructive.
+    spec = spec.copy()
+    nodes = spec.index()
+
+    topo_order = []
+    remaining = [name for name in nodes.keys() if not parents(nodes[name])]
+    heapify(remaining)
+
+    while remaining:
+        name = heappop(remaining)
+        topo_order.append(name)
+
+        node = nodes[name]
+        for dep in children(node).values():
+            del parents(dep)[node.name]
+            if not parents(dep):
+                heappush(remaining, dep.name)
+
+    if any(parents(s) for s in spec.traverse()):
+        raise ValueError("Spec has cycles!")
+    else:
+        return topo_order
+
+
+def find(seq, predicate):
+    """Find index in seq for which predicate is True.
+
+    Searches the sequence and returns the index of the element for
+    which the predicate evaluates to True.  Returns -1 if the
+    predicate does not evaluate to True for any element in seq.
+
+    """
+    for i, elt in enumerate(seq):
+        if predicate(elt):
+            return i
+    return -1
+
+
+# Names of different graph line states.  We Record previous line
+# states so that we can easily determine what to do when connecting.
+states = ('node', 'collapse', 'merge-right', 'expand-right', 'back-edge')
+NODE, COLLAPSE, MERGE_RIGHT, EXPAND_RIGHT, BACK_EDGE = states
+
+class AsciiGraph(object):
+    def __init__(self):
+        # These can be set after initialization or after a call to
+        # graph() to change behavior.
+        self.node_character = '*'
+        self.debug = False
+        self.indent = 0
+
+        # These are colors in the order they'll be used for edges.
+        # See llnl.util.tty.color for details on color characters.
+        self.colors = 'rgbmcyRGBMCY'
+
+        # Internal vars are used in the graph() function and are
+        # properly initialized there.
+        self._name_to_color = None    # Node name to color
+        self._out = None              # Output stream
+        self._frontier = None         # frontier
+        self._nodes = None            # dict from name -> node
+        self._prev_state = None       # State of previous line
+        self._prev_index = None       # Index of expansion point of prev line
+
+
+    def _indent(self):
+        self._out.write(self.indent * ' ')
+
+
+    def _write_edge(self, string, index, sub=0):
+        """Write a colored edge to the output stream."""
+        name = self._frontier[index][sub]
+        edge = "@%s{%s}" % (self._name_to_color[name], string)
+        self._out.write(edge)
+
+
+    def _connect_deps(self, i, deps, label=None):
+        """Connect dependencies to existing edges in the frontier.
+
+        ``deps`` are to be inserted at position i in the
+        frontier. This routine determines whether other open edges
+        should be merged with <deps> (if there are other open edges
+        pointing to the same place) or whether they should just be
+        inserted as a completely new open edge.
+
+        Open edges that are not fully expanded (i.e. those that point
+        at multiple places) are left intact.
+
+        Parameters:
+
+        label    -- optional debug label for the connection.
+
+        Returns: True if the deps were connected to another edge
+        (i.e. the frontier did not grow) and False if the deps were
+        NOT already in the frontier (i.e. they were inserted and the
+        frontier grew).
+
+        """
+        if len(deps) == 1 and deps in self._frontier:
+            j = self._frontier.index(deps)
+
+            # convert a right connection into a left connection
+            if i < j:
+                self._frontier.pop(j)
+                self._frontier.insert(i, deps)
+                return self._connect_deps(j, deps, label)
+
+            collapse = True
+            if self._prev_state == EXPAND_RIGHT:
+                # Special case where previous line expanded and i is off by 1.
+                self._back_edge_line([], j, i+1, True, label + "-1.5 " + str((i+1,j)))
+                collapse = False
+
+            else:
+                # Previous node also expanded here, so i is off by one.
+                if self._prev_state == NODE and self._prev_index < i:
+                    i += 1
+
+                if i-j > 1:
+                    # We need two lines to connect if distance > 1
+                    self._back_edge_line([], j,  i, True, label + "-1 " + str((i,j)))
+                    collapse = False
+
+            self._back_edge_line([j], -1, -1, collapse, label + "-2 " + str((i,j)))
+            return True
+
+        elif deps:
+            self._frontier.insert(i, deps)
+            return False
+
+
+    def _set_state(self, state, index, label=None):
+        if state not in states:
+            raise ValueError("Invalid graph state!")
+        self._prev_state = state
+        self._prev_index = index
+
+        if self.debug:
+            self._out.write(" " * 20)
+            self._out.write("%-20s" % (
+                str(self._prev_state) if self._prev_state else ''))
+            self._out.write("%-20s" % (str(label) if label else ''))
+            self._out.write("%s" % self._frontier)
+
+
+    def _back_edge_line(self, prev_ends, end, start, collapse, label=None):
+        """Write part of a backwards edge in the graph.
+
+        Writes single- or multi-line backward edges in an ascii graph.
+        For example, a single line edge::
+
+            | | | | o |
+            | | | |/ /  <-- single-line edge connects two nodes.
+            | | | o |
+
+        Or a multi-line edge (requires two calls to back_edge)::
+
+            | | | | o |
+            | |_|_|/ /   <-- multi-line edge crosses vertical edges.
+            |/| | | |
+            o | | | |
+
+        Also handles "pipelined" edges, where the same line contains
+        parts of multiple edges::
+
+                      o start
+            | |_|_|_|/|
+            |/| | |_|/| <-- this line has parts of 2 edges.
+            | | |/| | |
+            o   o
+
+        Arguments:
+
+        prev_ends -- indices in frontier of previous edges that need
+                     to be finished on this line.
+
+        end -- end of the current edge on this line.
+
+        start -- start index of the current edge.
+
+        collapse -- whether the graph will be collapsing (i.e. whether
+                    to slant the end of the line or keep it straight)
+
+        label -- optional debug label to print after the line.
+
+        """
+        def advance(to_pos, edges):
+            """Write edges up to <to_pos>."""
+            for i in range(self._pos, to_pos):
+                for e in edges():
+                    self._write_edge(*e)
+                self._pos += 1
+
+        flen = len(self._frontier)
+        self._pos = 0
+        self._indent()
+
+        for p in prev_ends:
+            advance(p,         lambda: [("| ", self._pos)] )
+            advance(p+1,       lambda: [("|/", self._pos)] )
+
+        if end >= 0:
+            advance(end + 1,   lambda: [("| ", self._pos)] )
+            advance(start - 1, lambda: [("|",  self._pos), ("_", end)] )
+        else:
+            advance(start - 1, lambda: [("| ", self._pos)] )
+
+        if start >= 0:
+            advance(start,     lambda: [("|",  self._pos), ("/", end)] )
+
+        if collapse:
+            advance(flen,      lambda: [(" /", self._pos)] )
+        else:
+            advance(flen,      lambda: [("| ", self._pos)] )
+
+        self._set_state(BACK_EDGE, end, label)
+        self._out.write("\n")
+
+
+    def _node_line(self, index, name):
+        """Writes a line with a node at index."""
+        self._indent()
+        for c in range(index):
+            self._write_edge("| ", c)
+
+        self._out.write("%s " % self.node_character)
+
+        for c in range(index+1, len(self._frontier)):
+            self._write_edge("| ", c)
+
+        self._out.write(" %s" % name)
+        self._set_state(NODE, index)
+        self._out.write("\n")
+
+
+    def _collapse_line(self, index):
+        """Write a collapsing line after a node was added at index."""
+        self._indent()
+        for c in range(index):
+            self._write_edge("| ", c)
+        for c in range(index, len(self._frontier)):
+            self._write_edge(" /", c)
+
+        self._set_state(COLLAPSE, index)
+        self._out.write("\n")
+
+
+    def _merge_right_line(self, index):
+        """Edge at index is same as edge to right.  Merge directly with '\'"""
+        self._indent()
+        for c in range(index):
+            self._write_edge("| ", c)
+        self._write_edge("|", index)
+        self._write_edge("\\", index+1)
+        for c in range(index+1, len(self._frontier)):
+            self._write_edge("| ", c )
+
+        self._set_state(MERGE_RIGHT, index)
+        self._out.write("\n")
+
+
+    def _expand_right_line(self, index):
+        self._indent()
+        for c in range(index):
+            self._write_edge("| ", c)
+
+        self._write_edge("|", index)
+        self._write_edge("\\", index+1)
+
+        for c in range(index+2, len(self._frontier)):
+            self._write_edge(" \\", c)
+
+        self._set_state(EXPAND_RIGHT, index)
+        self._out.write("\n")
+
+
+    def write(self, spec, **kwargs):
+        """Write out an ascii graph of the provided spec.
+
+        Arguments:
+        spec -- spec to graph.  This only handles one spec at a time.
+
+        Optional arguments:
+
+        out -- file object to write out to (default is sys.stdout)
+
+        color -- whether to write in color.  Default is to autodetect
+                 based on output file.
+
+        """
+        out = kwargs.get('out', None)
+        if not out:
+            out = sys.stdout
+
+        color = kwargs.get('color', None)
+        if not color:
+            color = out.isatty()
+        self._out = ColorStream(sys.stdout, color=color)
+
+        # We'll traverse the spec in topo order as we graph it.
+        topo_order = topological_sort(spec, reverse=True)
+
+        # Work on a copy to be nondestructive
+        spec = spec.copy()
+        self._nodes = spec.index()
+
+        # Colors associated with each node in the DAG.
+        # Edges are colored by the node they point to.
+        self._name_to_color = dict((name, self.colors[i % len(self.colors)])
+                                  for i, name in enumerate(topo_order))
+
+        # Frontier tracks open edges of the graph as it's written out.
+        self._frontier = [[spec.name]]
+        while self._frontier:
+            # Find an unexpanded part of frontier
+            i = find(self._frontier, lambda f: len(f) > 1)
+
+            if i >= 0:
+                # Expand frontier until there are enough columns for all children.
+
+                # Figure out how many back connections there are and
+                # sort them so we do them in order
+                back = []
+                for d in self._frontier[i]:
+                    b = find(self._frontier[:i], lambda f: f == [d])
+                    if b != -1:
+                        back.append((b, d))
+
+                # Do all back connections in sorted order so we can
+                # pipeline them and save space.
+                if back:
+                    back.sort()
+                    prev_ends = []
+                    for j, (b, d) in enumerate(back):
+                        self._frontier[i].remove(d)
+                        if i-b > 1:
+                            self._back_edge_line(prev_ends, b, i, False, 'left-1')
+                            del prev_ends[:]
+                        prev_ends.append(b)
+
+                    # Check whether we did ALL the deps as back edges,
+                    # in which case we're done.
+                    collapse = not self._frontier[i]
+                    if collapse:
+                        self._frontier.pop(i)
+                    self._back_edge_line(prev_ends, -1, -1, collapse, 'left-2')
+
+                elif len(self._frontier[i]) > 1:
+                    # Expand forward after doing all back connections
+
+                    if (i+1 < len(self._frontier) and len(self._frontier[i+1]) == 1
+                        and self._frontier[i+1][0] in self._frontier[i]):
+                        # We need to connect to the element to the right.
+                        # Keep lines straight by connecting directly and
+                        # avoiding unnecessary expand/contract.
+                        name = self._frontier[i+1][0]
+                        self._frontier[i].remove(name)
+                        self._merge_right_line(i)
+
+                    else:
+                        # Just allow the expansion here.
+                        name = self._frontier[i].pop(0)
+                        deps = [name]
+                        self._frontier.insert(i, deps)
+                        self._expand_right_line(i)
+
+                        self._frontier.pop(i)
+                        self._connect_deps(i, deps, "post-expand")
+
+
+                # Handle any remaining back edges to the right
+                j = i+1
+                while j < len(self._frontier):
+                    deps = self._frontier.pop(j)
+                    if not self._connect_deps(j, deps, "back-from-right"):
+                        j += 1
+
+            else:
+                # Nothing to expand; add dependencies for a node.
+                name = topo_order.pop()
+                node = self._nodes[name]
+
+                # Find the named node in the frontier and draw it.
+                i = find(self._frontier, lambda f: name in f)
+                self._node_line(i, name)
+
+                # Replace node with its dependencies
+                self._frontier.pop(i)
+                if node.dependencies:
+                    deps = sorted((d for d in node.dependencies), reverse=True)
+                    self._connect_deps(i, deps, "new-deps") # anywhere.
+
+                elif self._frontier:
+                    self._collapse_line(i)
+
+
+def graph_ascii(spec, **kwargs):
+    node_character = kwargs.get('node', 'o')
+    out            = kwargs.pop('out', None)
+    debug          = kwargs.pop('debug', False)
+    indent         = kwargs.pop('indent', 0)
+    color          = kwargs.pop('color', None)
+    check_kwargs(kwargs, graph_ascii)
+
+    graph = AsciiGraph()
+    graph.debug = debug
+    graph.indent = indent
+    graph.node_character = node_character
+
+    graph.write(spec, color=color, out=out)
+
+
+
+def graph_dot(*specs, **kwargs):
+    """Generate a graph in dot format of all provided specs.
+
+    Print out a dot formatted graph of all the dependencies between
+    package.  Output can be passed to graphviz, e.g.:
+
+        spack graph --dot qt | dot -Tpdf > spack-graph.pdf
+
+    """
+    out = kwargs.pop('out', sys.stdout)
+    check_kwargs(kwargs, graph_dot)
+
+    out.write('digraph G {\n')
+    out.write('  label = "Spack Dependencies"\n')
+    out.write('  labelloc = "b"\n')
+    out.write('  rankdir = "LR"\n')
+    out.write('  ranksep = "5"\n')
+    out.write('\n')
+
+    def quote(string):
+        return '"%s"' % string
+
+    if not specs:
+        specs = [p.name for p in spack.db.all_packages()]
+    else:
+        roots = specs
+        specs = set()
+        for spec in roots:
+            specs.update(Spec(s.name) for s in spec.normalized().traverse())
+
+    deps = []
+    for spec in specs:
+        out.write('  %-30s [label="%s"]\n' % (quote(spec.name), spec.name))
+
+        # Skip virtual specs (we'll find out about them from concrete ones.
+        if spec.virtual:
+            continue
+
+        # Add edges for each depends_on in the package.
+        for dep_name, dep in spec.package.dependencies.iteritems():
+            deps.append((spec.name, dep_name))
+
+        # If the package provides something, add an edge for that.
+        for provider in set(s.name for s in spec.package.provided):
+            deps.append((provider, spec.name))
+
+    out.write('\n')
+
+    for pair in deps:
+        out.write('  "%s" -> "%s"\n' % pair)
+    out.write('}\n')

lib/spack/spack/hooks/__init__.py

@@ -31,7 +31,9 @@
 
    Currently the following hooks are supported:
 
+      * pre_install()
       * post_install()
+      * pre_uninstall()
       * post_uninstall()
 
    This can be used to implement support for things like module
@@ -47,8 +49,11 @@
 def all_hook_modules():
     modules = []
     for name in list_modules(spack.hooks_path):
+        mod_name = __name__ + '.' + name
         path = join_path(spack.hooks_path, name) + ".py"
-        modules.append(imp.load_source('spack.hooks', path))
+        mod = imp.load_source(mod_name, path)
+        modules.append(mod)
+
     return modules
 
 
@@ -67,5 +72,8 @@ def __call__(self, pkg):
 #
 # Define some functions that can be called to fire off hooks.
 #
-post_install = HookRunner('post_install')
+pre_install    = HookRunner('pre_install')
+post_install   = HookRunner('post_install')
+
+pre_uninstall  = HookRunner('pre_uninstall')
 post_uninstall = HookRunner('post_uninstall')

lib/spack/spack/hooks/extensions.py

@@ -0,0 +1,36 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+import spack
+
+
+def pre_uninstall(pkg):
+    # Need to do this b/c uninstall does not automatically do it.
+    # TODO: store full graph info in stored .spec file.
+    pkg.spec.normalize()
+
+    if pkg.is_extension:
+        if pkg.activated:
+            pkg.do_deactivate(force=True)

lib/spack/spack/mirror.py

@@ -37,6 +37,7 @@
 
 import spack
 import spack.error
+import spack.url as url
 import spack.fetch_strategy as fs
 from spack.spec import Spec
 from spack.stage import Stage
@@ -45,14 +46,14 @@
 
 
 def mirror_archive_filename(spec):
-    """Get the path that this spec will live at within a mirror."""
+    """Get the name of the spec's archive in the mirror."""
     if not spec.version.concrete:
         raise ValueError("mirror.path requires spec with concrete version.")
 
     fetcher = spec.package.fetcher
     if isinstance(fetcher, fs.URLFetchStrategy):
         # If we fetch this version with a URLFetchStrategy, use URL's archive type
-        ext = extension(fetcher.url)
+        ext = url.downloaded_file_extension(fetcher.url)
     else:
         # Otherwise we'll make a .tar.gz ourselves
         ext = 'tar.gz'
@@ -60,6 +61,11 @@ def mirror_archive_filename(spec):
     return "%s-%s.%s" % (spec.package.name, spec.version, ext)
 
 
+def mirror_archive_path(spec):
+    """Get the relative path to the spec's archive within a mirror."""
+    return join_path(spec.name, mirror_archive_filename(spec))
+
+
 def get_matching_versions(specs, **kwargs):
     """Get a spec for EACH known version matching any spec in the list."""
     matching = []
@@ -140,12 +146,10 @@ def create(path, specs, **kwargs):
         stage = None
         try:
             # create a subdirectory for the current package@version
-            subdir = join_path(mirror_root, pkg.name)
+            archive_path = os.path.abspath(join_path(path, mirror_archive_path(spec)))
+            subdir = os.path.dirname(archive_path)
             mkdirp(subdir)
 
-            archive_file = mirror_archive_filename(spec)
-            archive_path = join_path(subdir, archive_file)
-
             if os.path.exists(archive_path):
                 tty.msg("Already added %s" % spec.format("$_$@"))
                 present.append(spec)

lib/spack/spack/modules.py

@@ -49,6 +49,7 @@
 import re
 import textwrap
 import shutil
+from glob import glob
 from contextlib import closing
 
 import llnl.util.tty as tty
@@ -123,6 +124,13 @@ def add_path(path_name, directory):
                 if os.path.isdir(directory):
                     add_path(var, directory)
 
+            # Add python path unless it's an actual python installation
+            # TODO: is there a better way to do this?
+            if self.spec.name != 'python':
+                site_packages = glob(join_path(self.spec.prefix.lib, "python*/site-packages"))
+                if site_packages:
+                    add_path('PYTHONPATH', site_packages[0])
+
             # short description is just the package + version
             # TODO: maybe packages can optionally provide it.
             self.short_description = self.spec.format("$_ $@")

lib/spack/spack/package.py

@@ -35,13 +35,17 @@
 """
 import os
 import re
+import time
 import inspect
 import subprocess
 import platform as py_platform
 import multiprocessing
-from urlparse import urlparse
+from urlparse import urlparse, urljoin
+import textwrap
+from StringIO import StringIO
 
 import llnl.util.tty as tty
+from llnl.util.link_tree import LinkTree
 from llnl.util.filesystem import *
 from llnl.util.lang import *
 
@@ -49,6 +53,7 @@
 import spack.spec
 import spack.error
 import spack.compilers
+import spack.mirror
 import spack.hooks
 import spack.build_environment as build_env
 import spack.url as url
@@ -57,6 +62,7 @@
 from spack.stage import Stage
 from spack.util.web import get_pages
 from spack.util.compression import allowed_archive, extension
+from spack.util.executable import ProcessError
 
 """Allowed URL schemes for spack packages."""
 _ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"]
@@ -282,10 +288,9 @@ class SomePackage(Package):
 
     .. code-block:: python
 
-       p.do_clean()              # runs make clean
-       p.do_clean_work()         # removes the build directory and
+       p.do_clean()              # removes the stage directory entirely
+       p.do_restage()            # removes the build directory and
                                  # re-expands the archive.
-       p.do_clean_dist()         # removes the stage directory entirely
 
     The convention used here is that a do_* function is intended to be called
     internally by Spack commands (in spack.cmd).  These aren't for package
@@ -316,12 +321,24 @@ class SomePackage(Package):
     """Patches to apply to newly expanded source, if any."""
     patches = {}
 
+    """Specs of package this one extends, or None.
+
+    Currently, ppackages can extend at most one other package.
+    """
+    extendees = {}
+
     #
     # These are default values for instance variables.
     #
     """By default we build in parallel.  Subclasses can override this."""
     parallel = True
 
+    """# jobs to use for parallel make. If set, overrides default of ncpus."""
+    make_jobs = None
+
+    """Most packages are NOT extendable.  Set to True if you want extensions."""
+    extendable = False
+
 
     def __init__(self, spec):
         # this determines how the package should be built.
@@ -333,9 +350,6 @@ def __init__(self, spec):
         if '.' in self.name:
             self.name = self.name[self.name.rindex('.') + 1:]
 
-        # This is set by scraping a web page.
-        self._available_versions = None
-
         # Sanity check some required variables that could be
         # overridden by package authors.
         def ensure_has_dict(attr_name):
@@ -368,12 +382,20 @@ def ensure_has_dict(attr_name):
         # stage used to build this package.
         self._stage = None
 
-        # If there's no default URL provided, set this package's url to None
-        if not hasattr(self, 'url'):
-            self.url = None
-
-        # Init fetch strategy to None
+        # Init fetch strategy and url to None
         self._fetcher = None
+        self.url = getattr(self.__class__, 'url', None)
+
+        # Fix up self.url if this package fetches with a URLFetchStrategy.
+        # This makes self.url behave sanely.
+        if self.spec.versions.concrete:
+            # TODO: this is a really roundabout way of determining the type
+            # TODO: of fetch to do. figure out a more sane fetch strategy/package
+            # TODO: init order (right now it's conflated with stage, package, and
+            # TODO: the tests make assumptions)
+            f = fs.for_package_version(self, self.version)
+            if isinstance(f, fs.URLFetchStrategy):
+                self.url = self.url_for_version(self.spec.version)
 
         # Set a default list URL (place to find available versions)
         if not hasattr(self, 'list_url'):
@@ -382,6 +404,13 @@ def ensure_has_dict(attr_name):
         if not hasattr(self, 'list_depth'):
             self.list_depth = 1
 
+        # Set up some internal variables for timing.
+        self._fetch_time = 0.0
+        self._total_time = 0.0
+
+        if self.is_extension:
+            spack.db.get(self.extendee_spec)._check_extendable()
+
 
     @property
     def version(self):
@@ -410,7 +439,7 @@ def nearest_url(self, version):
            *higher* URL, and if that isn't there raises an error.
         """
         version_urls = self.version_urls()
-        url = self.url
+        url = getattr(self.__class__, 'url', None)
 
         for v in version_urls:
             if v > version and url:
@@ -420,21 +449,15 @@ def nearest_url(self, version):
         return url
 
 
-    def has_url(self):
-        """Returns whether there is a URL available for this package.
-           If there isn't, it's probably fetched some other way (version
-           control, etc.)"""
-        return self.url or self.version_urls()
-
-
     # TODO: move this out of here and into some URL extrapolation module?
     def url_for_version(self, version):
         """Returns a URL that you can download a new version of this package from."""
         if not isinstance(version, Version):
             version = Version(version)
 
-        if not self.has_url():
-            raise NoURLError(self.__class__)
+        cls = self.__class__
+        if not (hasattr(cls, 'url') or self.version_urls()):
+            raise NoURLError(cls)
 
         # If we have a specific URL for this version, don't extrapolate.
         version_urls = self.version_urls()
@@ -452,12 +475,18 @@ def stage(self):
             raise ValueError("Can only get a stage for a concrete package.")
 
         if self._stage is None:
-            self._stage = Stage(self.fetcher,
-                                mirror_path=self.mirror_path(),
-                                name=self.spec.short_spec)
+            mp = spack.mirror.mirror_archive_path(self.spec)
+            self._stage = Stage(
+                self.fetcher, mirror_path=mp, name=self.spec.short_spec)
         return self._stage
 
 
+    @stage.setter
+    def stage(self, stage):
+        """Allow a stage object to be set to override the default."""
+        self._stage = stage
+
+
     @property
     def fetcher(self):
         if not self.spec.versions.concrete:
@@ -474,11 +503,45 @@ def fetcher(self, f):
         self._fetcher = f
 
 
-    def mirror_path(self):
-        """Get path to this package's archive in a mirror."""
-        filename = "%s-%s." % (self.name, self.version)
-        filename += extension(self.url) if self.has_url() else "tar.gz"
-        return "%s/%s" % (self.name, filename)
+    @property
+    def extendee_spec(self):
+        """Spec of the extendee of this package, or None if it is not an extension."""
+        if not self.extendees:
+            return None
+        name = next(iter(self.extendees))
+        if not name in self.spec:
+            spec, kwargs = self.extendees[name]
+            return spec
+
+        # Need to do this to get the concrete version of the spec
+        return self.spec[name]
+
+
+    @property
+    def extendee_args(self):
+        """Spec of the extendee of this package, or None if it is not an extension."""
+        if not self.extendees:
+            return None
+        name = next(iter(self.extendees))
+        return self.extendees[name][1]
+
+
+    @property
+    def is_extension(self):
+        return len(self.extendees) > 0
+
+
+    def extends(self, spec):
+        return (spec.name in self.extendees and
+                spec.satisfies(self.extendees[spec.name][0]))
+
+
+    @property
+    def activated(self):
+        if not self.is_extension:
+            raise ValueError("is_extension called on package that is not an extension.")
+        exts = spack.install_layout.extension_map(self.extendee_spec)
+        return (self.name in exts) and (exts[self.name] == self.spec)
 
 
     def preorder_traversal(self, visited=None, **kwargs):
@@ -611,14 +674,26 @@ def do_fetch(self):
         if not self.spec.concrete:
             raise ValueError("Can only fetch concrete packages.")
 
+        start_time = time.time()
         if spack.do_checksum and not self.version in self.versions:
-            raise FetchError(
-                "Cannot fetch %s safely; there is no checksum on file for version %s."
-                % (self.name, self.version),
-                "Add a checksum to the package file, or use --no-checksum to "
-                "skip this check.")
+            tty.warn("There is no checksum on file to fetch %s safely."
+                     % self.spec.format('$_$@'))
+
+            # Ask the user whether to skip the checksum if we're
+            # interactive, but just fail if non-interactive.
+            checksum_msg = "Add a checksum or use --no-checksum to skip this check."
+            ignore_checksum = False
+            if sys.stdout.isatty():
+                ignore_checksum = tty.get_yes_or_no("  Fetch anyway?", default=False)
+                if ignore_checksum:
+                    tty.msg("Fetching with no checksum.", checksum_msg)
+
+            if not ignore_checksum:
+                raise FetchError(
+                    "Will not fetch %s." % self.spec.format('$_$@'), checksum_msg)
 
         self.stage.fetch()
+        self._fetch_time = time.time() - start_time
 
         if spack.do_checksum and self.version in self.versions:
             self.stage.check()
@@ -650,8 +725,11 @@ def do_patch(self):
         # Kick off the stage first.
         self.do_stage()
 
+        # Package can add its own patch function.
+        has_patch_fun = hasattr(self, 'patch') and callable(self.patch)
+
         # If there are no patches, note it.
-        if not self.patches:
+        if not self.patches and not has_patch_fun:
             tty.msg("No patches needed for %s." % self.name)
             return
 
@@ -674,7 +752,7 @@ def do_patch(self):
             tty.msg("Already patched %s" % self.name)
             return
 
-        # Apply all the patches for specs that match this on
+        # Apply all the patches for specs that match this one
         for spec, patch_list in self.patches.items():
             if self.spec.satisfies(spec):
                 for patch in patch_list:
@@ -692,15 +770,33 @@ def do_patch(self):
             os.remove(bad_file)
         touch(good_file)
 
+        if has_patch_fun:
+            self.patch()
+
+        tty.msg("Patched %s" % self.name)
+
+
+    def do_fake_install(self):
+        """Make a fake install directory contaiing a 'fake' file in bin."""
+        mkdirp(self.prefix.bin)
+        touch(join_path(self.prefix.bin, 'fake'))
+        mkdirp(self.prefix.lib)
+        mkdirp(self.prefix.man1)
+
 
     def do_install(self, **kwargs):
         """This class should call this version of the install method.
            Package implementations should override install().
         """
         # whether to keep the prefix on failure.  Default is to destroy it.
-        keep_prefix = kwargs.get('keep_prefix', False)
-        keep_stage  = kwargs.get('keep_stage', False)
-        ignore_deps = kwargs.get('ignore_deps', False)
+        keep_prefix  = kwargs.get('keep_prefix', False)
+        keep_stage   = kwargs.get('keep_stage',  False)
+        ignore_deps  = kwargs.get('ignore_deps', False)
+        fake_install = kwargs.get('fake',        False)
+        skip_patch   = kwargs.get('skip_patch',  False)
+
+        # Override builtin number of make jobs.
+        self.make_jobs    = kwargs.get('make_jobs',   None)
 
         if not self.spec.concrete:
             raise ValueError("Can only install concrete packages.")
@@ -709,85 +805,99 @@ def do_install(self, **kwargs):
             tty.msg("%s is already installed in %s." % (self.name, self.prefix))
             return
 
+        tty.msg("Installing %s" % self.name)
+
         if not ignore_deps:
-            self.do_install_dependencies()
+            self.do_install_dependencies(**kwargs)
 
-        self.do_patch()
+        start_time = time.time()
+        if not fake_install:
+            if not skip_patch:
+                self.do_patch()
+            else:
+                self.do_stage()
 
-        # Fork a child process to do the build.  This allows each
-        # package authors to have full control over their environment,
-        # etc. without offecting other builds that might be executed
-        # in the same spack call.
-        try:
-            pid = os.fork()
-        except OSError, e:
-            raise InstallError("Unable to fork build process: %s" % e)
+        # create the install directory.  The install layout
+        # handles this in case so that it can use whatever
+        # package naming scheme it likes.
+        spack.install_layout.make_path_for_spec(self.spec)
 
-        if pid == 0:
+        def cleanup():
+            if not keep_prefix:
+                # If anything goes wrong, remove the install prefix
+                self.remove_prefix()
+            else:
+                tty.warn("Keeping install prefix in place despite error.",
+                         "Spack will think this package is installed." +
+                         "Manually remove this directory to fix:",
+                         self.prefix)
+
+        def real_work():
             try:
                 tty.msg("Building %s." % self.name)
 
-                # create the install directory.  The install layout
-                # handles this in case so that it can use whatever
-                # package naming scheme it likes.
-                spack.install_layout.make_path_for_spec(self.spec)
+                # Run the pre-install hook in the child process after
+                # the directory is created.
+                spack.hooks.pre_install(self)
 
                 # Set up process's build environment before running install.
-                build_env.set_compiler_environment_variables(self)
-                build_env.set_build_environment_variables(self)
-                build_env.set_module_variables_for_package(self)
-
-                # Subclasses implement install() to do the real work.
-                self.install(self.spec, self.prefix)
+                self.stage.chdir_to_source()
+                if fake_install:
+                    self.do_fake_install()
+                else:
+                    # Subclasses implement install() to do the real work.
+                    self.install(self.spec, self.prefix)
 
                 # Ensure that something was actually installed.
-                if not os.listdir(self.prefix):
-                    raise InstallError(
-                        "Install failed for %s.  Nothing was installed!"
-                        % self.name)
+                self._sanity_check_install()
 
                 # On successful install, remove the stage.
                 if not keep_stage:
                     self.stage.destroy()
 
-                tty.msg("Successfully installed %s" % self.name)
+                # Stop timer.
+                self._total_time = time.time() - start_time
+                build_time = self._total_time - self._fetch_time
+
+                tty.msg("Successfully installed %s." % self.name,
+                        "Fetch: %s.  Build: %s.  Total: %s."
+                        % (_hms(self._fetch_time), _hms(build_time), _hms(self._total_time)))
                 print_pkg(self.prefix)
 
-                # Use os._exit here to avoid raising a SystemExit exception,
-                # which interferes with unit tests.
-                os._exit(0)
+            except ProcessError, e:
+                # One of the processes returned an error code.
+                # Suppress detailed stack trace here unless in debug mode
+                if spack.debug:
+                    raise e
+                else:
+                    tty.error(e)
+
+                # Still need to clean up b/c there was an error.
+                cleanup()
 
             except:
-                if not keep_prefix:
-                    # If anything goes wrong, remove the install prefix
-                    self.remove_prefix()
-                else:
-                    tty.warn("Keeping install prefix in place despite error.",
-                             "Spack will think this package is installed." +
-                             "Manually remove this directory to fix:",
-                             self.prefix)
-
-                # Child doesn't raise or return to main spack code.
-                # Just runs default exception handler and exits.
-                sys.excepthook(*sys.exc_info())
-                os._exit(1)
-
-        # Parent process just waits for the child to complete.  If the
-        # child exited badly, assume it already printed an appropriate
-        # message.  Just make the parent exit with an error code.
-        pid, returncode = os.waitpid(pid, 0)
-        if returncode != 0:
-            sys.exit(1)
+                # other exceptions just clean up and raise.
+                cleanup()
+                raise
 
+        build_env.fork(self, real_work)
 
         # Once everything else is done, run post install hooks
         spack.hooks.post_install(self)
 
 
-    def do_install_dependencies(self):
+    def _sanity_check_install(self):
+        installed = set(os.listdir(self.prefix))
+        installed.difference_update(spack.install_layout.hidden_file_paths)
+        if not installed:
+            raise InstallError(
+                "Install failed for %s.  Nothing was installed!" % self.name)
+
+
+    def do_install_dependencies(self, **kwargs):
         # Pass along paths of dependencies here
         for dep in self.spec.dependencies.values():
-            dep.package.do_install()
+            dep.package.do_install(**kwargs)
 
 
     @property
@@ -799,6 +909,32 @@ def module(self):
                           fromlist=[self.__class__.__name__])
 
 
+    def setup_dependent_environment(self, module, spec, dependent_spec):
+        """Called before the install() method of dependents.
+
+        Default implementation does nothing, but this can be
+        overridden by an extendable package to set up the install
+        environment for its extensions.  This is useful if there are
+        some common steps to installing all extensions for a
+        certain package.
+
+        Some examples:
+
+        1. Installing python modules generally requires PYTHONPATH to
+           point to the lib/pythonX.Y/site-packages directory in the
+           module's install prefix.  This could set that variable.
+
+        2. Extensions often need to invoke the 'python' interpreter
+           from the Python installation being extended.  This routine can
+           put a 'python' Execuable object in the module scope for the
+           extension package to simplify extension installs.
+
+        3. A lot of Qt extensions need QTDIR set.  This can be used to do that.
+
+        """
+        pass
+
+
     def install(self, spec, prefix):
         """Package implementations override this with their own build configuration."""
         raise InstallError("Package %s provides no install method!" % self.name)
@@ -818,6 +954,10 @@ def do_uninstall(self, **kwargs):
                 "The following installed packages depend on it: %s" %
                 ' '.join(formatted_deps))
 
+        # Pre-uninstall hook runs first.
+        spack.hooks.pre_uninstall(self)
+
+        # Uninstalling in Spack only requires removing the prefix.
         self.remove_prefix()
         tty.msg("Successfully uninstalled %s." % self.spec.short_spec)
 
@@ -825,95 +965,227 @@ def do_uninstall(self, **kwargs):
         spack.hooks.post_uninstall(self)
 
 
-    def do_clean(self):
-        if self.stage.expanded_archive_path:
-            self.stage.chdir_to_source()
-            self.clean()
+    def _check_extendable(self):
+        if not self.extendable:
+            raise ValueError("Package %s is not extendable!" % self.name)
 
 
-    def clean(self):
-        """By default just runs make clean.  Override if this isn't good."""
-        # TODO: should we really call make clean, ro just blow away the directory?
-        make = build_env.MakeExecutable('make', self.parallel)
-        make('clean')
+    def _sanity_check_extension(self):
+        if not self.is_extension:
+            raise ActivationError("This package is not an extension.")
+
+        extendee_package = self.extendee_spec.package
+        extendee_package._check_extendable()
+
+        if not extendee_package.installed:
+            raise ActivationError("Can only (de)activate extensions for installed packages.")
+        if not self.installed:
+            raise ActivationError("Extensions must first be installed.")
+        if not self.extendee_spec.name in self.extendees:
+            raise ActivationError("%s does not extend %s!" % (self.name, self.extendee.name))
 
 
-    def do_clean_work(self):
-        """By default just blows away the stage directory and re-stages."""
+    def do_activate(self, **kwargs):
+        """Called on an etension to invoke the extendee's activate method.
+
+        Commands should call this routine, and should not call
+        activate() directly.
+        """
+        self._sanity_check_extension()
+        force = kwargs.get('force', False)
+
+        # TODO: get rid of this normalize - DAG handling.
+        self.spec.normalize()
+
+        spack.install_layout.check_extension_conflict(self.extendee_spec, self.spec)
+
+        if not force:
+            for spec in self.spec.traverse(root=False):
+                if spec.package.extends(self.extendee_spec):
+                    # TODO: fix this normalize() requirement -- revisit DAG handling.
+                    spec.package.spec.normalize()
+                    if not spec.package.activated:
+                        spec.package.do_activate(**kwargs)
+
+        self.extendee_spec.package.activate(self, **self.extendee_args)
+
+        spack.install_layout.add_extension(self.extendee_spec, self.spec)
+        tty.msg("Activated extension %s for %s."
+                % (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
+
+
+    def activate(self, extension, **kwargs):
+        """Symlinks all files from the extension into extendee's install dir.
+
+        Package authors can override this method to support other
+        extension mechanisms.  Spack internals (commands, hooks, etc.)
+        should call do_activate() method so that proper checks are
+        always executed.
+
+        """
+        def ignore(filename):
+            return (filename in spack.install_layout.hidden_file_paths or
+                    kwargs.get('ignore', lambda f: False)(filename))
+
+        tree = LinkTree(extension.prefix)
+        conflict = tree.find_conflict(self.prefix, ignore=ignore)
+        if conflict:
+            raise ExtensionConflictError(conflict)
+        tree.merge(self.prefix, ignore=ignore)
+
+
+    def do_deactivate(self, **kwargs):
+        """Called on the extension to invoke extendee's deactivate() method."""
+        self._sanity_check_extension()
+        force = kwargs.get('force', False)
+
+        # Allow a force deactivate to happen.  This can unlink
+        # spurious files if something was corrupted.
+        if not force:
+            spack.install_layout.check_activated(self.extendee_spec, self.spec)
+
+            activated = spack.install_layout.extension_map(self.extendee_spec)
+            for name, aspec in activated.items():
+                if aspec != self.spec and self.spec in aspec:
+                    raise ActivationError(
+                        "Cannot deactivate %s beacuse %s is activated and depends on it."
+                        % (self.spec.short_spec, aspec.short_spec))
+
+        self.extendee_spec.package.deactivate(self, **self.extendee_args)
+
+        # redundant activation check -- makes SURE the spec is not
+        # still activated even if something was wrong above.
+        if self.activated:
+            spack.install_layout.remove_extension(self.extendee_spec, self.spec)
+
+        tty.msg("Deactivated extension %s for %s."
+                % (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
+
+
+    def deactivate(self, extension, **kwargs):
+        """Unlinks all files from extension out of this package's install dir.
+
+        Package authors can override this method to support other
+        extension mechanisms.  Spack internals (commands, hooks, etc.)
+        should call do_deactivate() method so that proper checks are
+        always executed.
+
+        """
+        def ignore(filename):
+            return (filename in spack.install_layout.hidden_file_paths or
+                    kwargs.get('ignore', lambda f: False)(filename))
+
+        tree = LinkTree(extension.prefix)
+        tree.unmerge(self.prefix, ignore=ignore)
+
+
+    def do_restage(self):
+        """Reverts expanded/checked out source to a pristine state."""
         self.stage.restage()
 
 
-    def do_clean_dist(self):
-        """Removes the stage directory where this package was built."""
+    def do_clean(self):
+        """Removes the package's build stage and source tarball."""
         if os.path.exists(self.stage.path):
             self.stage.destroy()
 
 
-    def fetch_available_versions(self):
-        if not hasattr(self, 'url'):
-            raise VersionFetchError(self.__class__)
+    def format_doc(self, **kwargs):
+        """Wrap doc string at 72 characters and format nicely"""
+        indent = kwargs.get('indent', 0)
 
-        # If not, then try to fetch using list_url
-        if not self._available_versions:
-            try:
-                self._available_versions = find_versions_of_archive(
-                    self.url,
-                    list_url=self.list_url,
-                    list_depth=self.list_depth)
+        if not self.__doc__:
+            return ""
 
-                if not self._available_versions:
-                    tty.warn("Found no versions for %s" % self.name,
-                             "Check the list_url and list_depth attribute on the "
-                             + self.name + " package.",
-                             "Use them to tell Spack where to look for versions.")
-
-            except spack.error.NoNetworkConnectionError, e:
-                tty.die("Package.fetch_available_versions couldn't connect to:",
-                        e.url, e.message)
-
-        return self._available_versions
+        doc = re.sub(r'\s+', ' ', self.__doc__)
+        lines = textwrap.wrap(doc, 72)
+        results = StringIO()
+        for line in lines:
+            results.write((" " * indent) + line + "\n")
+        return results.getvalue()
 
 
     @property
-    def available_versions(self):
-        # If the package overrode available_versions, then use that.
-        if self.versions is not None:
-            return VersionList(self.versions.keys())
-        else:
-            vlist = self.fetch_available_versions()
-            if not vlist:
-                vlist = ver([self.version])
-            return vlist
+    def all_urls(self):
+        urls = []
+        if self.url:
+            urls.append(self.url)
+
+        for args in self.versions.values():
+            if 'url' in args:
+                urls.append(args['url'])
+        return urls
 
 
-def find_versions_of_archive(archive_url, **kwargs):
+    def fetch_remote_versions(self):
+        """Try to find remote versions of this package using the
+           list_url and any other URLs described in the package file."""
+        if not self.all_urls:
+            raise VersionFetchError(self.__class__)
+
+        try:
+            return find_versions_of_archive(
+                *self.all_urls, list_url=self.list_url, list_depth=self.list_depth)
+        except spack.error.NoNetworkConnectionError, e:
+            tty.die("Package.fetch_versions couldn't connect to:",
+                    e.url, e.message)
+
+
+    @property
+    def rpath(self):
+        """Get the rpath this package links with, as a list of paths."""
+        rpaths = [self.prefix.lib, self.prefix.lib64]
+        rpaths.extend(d.prefix.lib for d in self.spec.traverse(root=False)
+                      if os.path.isdir(d.prefix.lib))
+        rpaths.extend(d.prefix.lib64 for d in self.spec.traverse(root=False)
+                      if os.path.isdir(d.prefix.lib64))
+        return rpaths
+
+
+    @property
+    def rpath_args(self):
+        """Get the rpath args as a string, with -Wl,-rpath= for each element."""
+        return " ".join("-Wl,-rpath=%s" % p for p in self.rpath)
+
+
+def find_versions_of_archive(*archive_urls, **kwargs):
     list_url   = kwargs.get('list_url', None)
     list_depth = kwargs.get('list_depth', 1)
 
-    if not list_url:
-        list_url = url.find_list_url(archive_url)
-
-    # This creates a regex from the URL with a capture group for the
-    # version part of the URL.  The capture group is converted to a
-    # generic wildcard, so we can use this to extract things on a page
-    # that look like archive URLs.
-    url_regex = url.wildcard_version(archive_url)
-
-    # We'll be a bit more liberal and just look for the archive part,
-    # not the full path.
-    archive_regex = os.path.basename(url_regex)
+    # Generate a list of list_urls based on archive urls and any
+    # explicitly listed list_url in the package
+    list_urls = set()
+    if list_url:
+        list_urls.add(list_url)
+    for aurl in archive_urls:
+        list_urls.add(url.find_list_url(aurl))
 
     # Grab some web pages to scrape.
-    page_map = get_pages(list_url, depth=list_depth)
+    page_map = {}
+    for lurl in list_urls:
+        page_map.update(get_pages(lurl, depth=list_depth))
+
+    # Scrape them for archive URLs
+    regexes = []
+    for aurl in archive_urls:
+        # This creates a regex from the URL with a capture group for
+        # the version part of the URL.  The capture group is converted
+        # to a generic wildcard, so we can use this to extract things
+        # on a page that look like archive URLs.
+        url_regex = url.wildcard_version(aurl)
+
+        # We'll be a bit more liberal and just look for the archive
+        # part, not the full path.
+        regexes.append(os.path.basename(url_regex))
 
     # Build a version list from all the matches we find
-    versions = VersionList()
-    for site, page in page_map.iteritems():
+    versions = {}
+    for page_url, content in page_map.iteritems():
         # extract versions from matches.
-        matches = re.finditer(archive_regex, page)
-        version_strings = set(m.group(1) for m in matches)
-        for v in version_strings:
-            versions.add(Version(v))
+        for regex in regexes:
+            versions.update(
+                (Version(m.group(1)), urljoin(page_url, m.group(0)))
+                for m in re.finditer(regex, content))
 
     return versions
 
@@ -930,15 +1202,23 @@ def validate_package_url(url_string):
 
 def print_pkg(message):
     """Outputs a message with a package icon."""
-    mac_ver = py_platform.mac_ver()[0]
-    if mac_ver and Version(mac_ver) >= Version('10.7'):
-        print u"\U0001F4E6" + tty.indent,
-    else:
-        from llnl.util.tty.color import cwrite
-        cwrite('@*g{[+]} ')
+    from llnl.util.tty.color import cwrite
+    cwrite('@*g{[+]} ')
     print message
 
 
+def _hms(seconds):
+    """Convert time in seconds to hours, minutes, seconds."""
+    m, s = divmod(seconds, 60)
+    h, m = divmod(m, 60)
+
+    parts = []
+    if h: parts.append("%dh" % h)
+    if m: parts.append("%dm" % m)
+    if s: parts.append("%.2fs" % s)
+    return ' '.join(parts)
+
+
 class FetchError(spack.error.SpackError):
     """Raised when something goes wrong during fetch."""
     def __init__(self, message, long_msg=None):
@@ -976,8 +1256,8 @@ class VersionFetchError(PackageError):
     """Raised when a version URL cannot automatically be determined."""
     def __init__(self, cls):
         super(VersionFetchError, self).__init__(
-            "Cannot fetch version for package %s " % cls.__name__ +
-            "because it does not define a default url.")
+            "Cannot fetch versions for package %s " % cls.__name__ +
+            "because it does not define any URLs to fetch.")
 
 
 class NoURLError(PackageError):
@@ -985,3 +1265,17 @@ class NoURLError(PackageError):
     def __init__(self, cls):
         super(NoURLError, self).__init__(
             "Package %s has no version with a URL." % cls.__name__)
+
+
+class ExtensionError(PackageError): pass
+
+
+class ExtensionConflictError(ExtensionError):
+    def __init__(self, path):
+        super(ExtensionConflictError, self).__init__(
+            "Extension blocked by file: %s" % path)
+
+
+class ActivationError(ExtensionError):
+    def __init__(self, msg, long_msg=None):
+        super(ActivationError, self).__init__(msg, long_msg)

lib/spack/spack/packages.py

@@ -30,7 +30,7 @@
 
 import llnl.util.tty as tty
 from llnl.util.filesystem import join_path
-from llnl.util.lang import memoized
+from llnl.util.lang import *
 
 import spack.error
 import spack.spec
@@ -74,8 +74,11 @@ def get(self, spec, **kwargs):
         if not spec in self.instances:
             package_class = self.get_class_for_package_name(spec.name)
             try:
-                self.instances[spec.copy()] = package_class(spec)
+                copy = spec.copy()
+                self.instances[copy] = package_class(copy)
             except Exception, e:
+                if spack.debug:
+                    sys.excepthook(*sys.exc_info())
                 raise FailedConstructorError(spec.name, e)
 
         return self.instances[spec]
@@ -109,6 +112,24 @@ def providers_for(self, vpkg_spec):
         return providers
 
 
+    @_autospec
+    def extensions_for(self, extendee_spec):
+        return [p for p in self.all_packages() if p.extends(extendee_spec)]
+
+
+    @_autospec
+    def installed_extensions_for(self, extendee_spec):
+        for s in self.installed_package_specs():
+            try:
+                if s.package.extends(extendee_spec):
+                    yield s.package
+            except UnknownPackageError, e:
+                # Skip packages we know nothing about
+                continue
+                # TODO: add some conditional way to do this instead of
+                # catching exceptions.
+
+
     def dirname_for_package_name(self, pkg_name):
         """Get the directory name for a particular package.  This is the
            directory that contains its package.py file."""
@@ -171,6 +192,7 @@ def all_packages(self):
             yield self.get(name)
 
 
+    @memoized
     def exists(self, pkg_name):
         """Whether a package with the supplied name exists ."""
         return os.path.exists(self.filename_for_package_name(pkg_name))
@@ -213,38 +235,6 @@ def get_class_for_package_name(self, pkg_name):
         return cls
 
 
-    def graph_dependencies(self, out=sys.stdout):
-        """Print out a graph of all the dependencies between package.
-           Graph is in dot format."""
-        out.write('digraph G {\n')
-        out.write('  label = "Spack Dependencies"\n')
-        out.write('  labelloc = "b"\n')
-        out.write('  rankdir = "LR"\n')
-        out.write('  ranksep = "5"\n')
-        out.write('\n')
-
-        def quote(string):
-            return '"%s"' % string
-
-        deps = []
-        for pkg in self.all_packages():
-            out.write('  %-30s [label="%s"]\n' % (quote(pkg.name), pkg.name))
-
-            # Add edges for each depends_on in the package.
-            for dep_name, dep in pkg.dependencies.iteritems():
-                deps.append((pkg.name, dep_name))
-
-            # If the package provides something, add an edge for that.
-            for provider in set(p.name for p in pkg.provided):
-                deps.append((provider, pkg.name))
-
-        out.write('\n')
-
-        for pair in deps:
-            out.write('  "%s" -> "%s"\n' % pair)
-        out.write('}\n')
-
-
 class UnknownPackageError(spack.error.SpackError):
     """Raised when we encounter a package spack doesn't have."""
     def __init__(self, name):

lib/spack/spack/relations.py

@@ -68,7 +68,7 @@ class Mpileaks(Package):
         spack install mpileaks ^mvapich
         spack install mpileaks ^mpich
 """
-__all__ = [ 'depends_on', 'provides', 'patch', 'version' ]
+__all__ = [ 'depends_on', 'extends', 'provides', 'patch', 'version' ]
 
 import re
 import inspect
@@ -107,8 +107,9 @@ def depends_on(*specs):
     """Adds a dependencies local variable in the locals of
        the calling class, based on args. """
     pkg = get_calling_package_name()
+    clocals = caller_locals()
+    dependencies = clocals.setdefault('dependencies', {})
 
-    dependencies = caller_locals().setdefault('dependencies', {})
     for string in specs:
         for spec in spack.spec.parse(string):
             if pkg == spec.name:
@@ -116,6 +117,34 @@ def depends_on(*specs):
             dependencies[spec.name] = spec
 
 
+def extends(spec, **kwargs):
+    """Same as depends_on, but dependency is symlinked into parent prefix.
+
+    This is for Python and other language modules where the module
+    needs to be installed into the prefix of the Python installation.
+    Spack handles this by installing modules into their own prefix,
+    but allowing ONE module version to be symlinked into a parent
+    Python install at a time.
+
+    keyword arguments can be passed to extends() so that extension
+    packages can pass parameters to the extendee's extension
+    mechanism.
+
+    """
+    pkg = get_calling_package_name()
+    clocals = caller_locals()
+    dependencies = clocals.setdefault('dependencies', {})
+    extendees = clocals.setdefault('extendees', {})
+    if extendees:
+        raise RelationError("Packages can extend at most one other package.")
+
+    spec = Spec(spec)
+    if pkg == spec.name:
+        raise CircularReferenceError('extends', pkg)
+    dependencies[spec.name] = spec
+    extendees[spec.name] = (spec, kwargs)
+
+
 def provides(*specs, **kwargs):
     """Allows packages to provide a virtual dependency.  If a package provides
        'mpi', other packages can declare that they depend on "mpi", and spack

lib/spack/spack/spec.py

@@ -552,6 +552,13 @@ def short_spec(self):
         return self.format('$_$@$%@$+$=$#')
 
 
+    @property
+    def cshort_spec(self):
+        """Returns a version of the spec with the dependencies hashed
+           instead of completely enumerated."""
+        return self.format('$_$@$%@$+$=$#', color=True)
+
+
     @property
     def prefix(self):
         return Prefix(spack.install_layout.path_for_spec(self))
@@ -712,6 +719,15 @@ def flat_dependencies(self, **kwargs):
             raise InconsistentSpecError("Invalid Spec DAG: %s" % e.message)
 
 
+    def index(self):
+        """Return DependencyMap that points to all the dependencies in this
+           spec."""
+        dm = DependencyMap()
+        for spec in self.traverse():
+            dm[spec.name] = spec
+        return dm
+
+
     def flatten(self):
         """Pull all dependencies up to the root (this spec).
            Merge constraints for dependencies with the same name, and if they
@@ -858,7 +874,7 @@ def normalize(self, **kwargs):
     def normalized(self):
         """Return a normalized copy of this spec without modifying this spec."""
         clone = self.copy()
-        clone.normalized()
+        clone.normalize()
         return clone
 
 
@@ -1096,8 +1112,9 @@ def __getitem__(self, name):
 
 
     def __contains__(self, spec):
-        """True if this spec has any dependency that satisfies the supplied
-           spec."""
+        """True if this spec satisfis the provided spec, or if any dependency
+           does.  If the spec has no name, then we parse this one first.
+        """
         spec = self._autospec(spec)
         for s in self.traverse():
             if s.satisfies(spec):
@@ -1288,12 +1305,13 @@ def __str__(self):
     def tree(self, **kwargs):
         """Prints out this spec and its dependencies, tree-formatted
            with indentation."""
-        color  = kwargs.get('color', False)
-        depth  = kwargs.get('depth', False)
-        showid = kwargs.get('ids',   False)
-        cover  = kwargs.get('cover', 'nodes')
-        indent = kwargs.get('indent', 0)
-        format = kwargs.get('format', '$_$@$%@$+$=')
+        color  = kwargs.pop('color', False)
+        depth  = kwargs.pop('depth', False)
+        showid = kwargs.pop('ids',   False)
+        cover  = kwargs.pop('cover', 'nodes')
+        indent = kwargs.pop('indent', 0)
+        fmt    = kwargs.pop('format', '$_$@$%@$+$=')
+        check_kwargs(kwargs, self.tree)
 
         out = ""
         cur_id = 0
@@ -1310,7 +1328,7 @@ def tree(self, **kwargs):
             out += ("    " * d)
             if d > 0:
                 out += "^"
-            out += node.format(format, color=color) + "\n"
+            out += node.format(fmt, color=color) + "\n"
         return out
 
 

lib/spack/spack/stage.py

@@ -257,8 +257,11 @@ def fetch(self):
                 fetcher.fetch()
                 break
             except spack.error.SpackError, e:
-                tty.msg("Fetching %s failed." % fetcher)
+                tty.msg("Fetching from %s failed." % fetcher)
+                tty.debug(e)
                 continue
+        else:
+            tty.die("All fetchers failed for %s" % self.name)
 
 
     def check(self):
@@ -306,6 +309,39 @@ def destroy(self):
             os.chdir(os.path.dirname(self.path))
 
 
+class DIYStage(object):
+    """Simple class that allows any directory to be a spack stage."""
+    def __init__(self, path):
+        self.archive_file = None
+        self.path = path
+        self.source_path = path
+
+    def chdir(self):
+        if os.path.isdir(self.path):
+            os.chdir(self.path)
+        else:
+            tty.die("Setup failed: no such directory: " + self.path)
+
+    def chdir_to_source(self):
+        self.chdir()
+
+    def fetch(self):
+        tty.msg("No need to fetch for DIY.")
+
+    def check(self):
+        tty.msg("No checksum needed for DIY.")
+
+    def expand_archive(self):
+        tty.msg("Using source directory: %s" % self.source_path)
+
+    def restage(self):
+        tty.die("Cannot restage DIY stage.")
+
+    def destroy(self):
+        # No need to destroy DIY stage.
+        pass
+
+
 def _get_mirrors():
     """Get mirrors from spack configuration."""
     config = spack.config.get_config()