SPACK-87: enable disabled git fetch tests.

- remove spurious mutually exclusive group from subparser.

README.md

@@ -32,6 +32,36 @@ 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.

bin/spack

@@ -49,25 +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.')
-parser.add_argument('-V', '--version', action='version',
-                    version="%s" % spack.spack_version)
-parser.add_argument('-v', '--verbose', action='store_true',
-                    help="Print additional output during builds")
+    formatter_class=argparse.RawTextHelpFormatter,
+    description="Spack: the Supercomputing PACKage Manager." + colorize("""
+
+spec expressions:
+  PACKAGE [CONSTRAINTS]
+
+    CONSTRAINTS:
+      @c{@version}
+      @g{%compiler  @compiler_version}
+      @B{+variant}
+      @r{-variant} or @r{~variant}
+      @m{=architecture}
+      [^DEPENDENCY [CONSTRAINTS] ...]"""))
+
 parser.add_argument('-d', '--debug', action='store_true',
                     help="Write out debug logs during compile")
 parser.add_argument('-k', '--insecure', action='store_true',
-                    help="Do not check ssl certificates when downloading archives.")
+                    help="Do not check ssl certificates when downloading.")
 parser.add_argument('-m', '--mock', action='store_true',
                     help="Use mock packages instead of real ones.")
 parser.add_argument('-p', '--profile', action='store_true',
                     help="Profile execution using cProfile.")
+parser.add_argument('-v', '--verbose', action='store_true',
+                    help="Print additional output during builds")
+parser.add_argument('-V', '--version', action='version',
+                    version="%s" % spack.spack_version)
 
 # each command module implements a parser() function, to which we pass its
 # subparser for setup.

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 @@
-.font-smooth,.icon:before{-webkit-font-smoothing:antialiased}.clearfix{*zoom:1}.clearfix:before,.clearfix:after{display:table;content:""}.clearfix:after{clear:both}@font-face{font-family:fontawesome-webfont;font-weight:normal;font-style:normal;src:url("../font/fontawesome_webfont.eot");src:url("../font/fontawesome_webfont.eot?#iefix") format("embedded-opentype"),url("../font/fontawesome_webfont.woff") format("woff"),url("../font/fontawesome_webfont.ttf") format("truetype"),url("../font/fontawesome_webfont.svg#fontawesome-webfont") format("svg")}.icon:before{display:inline-block;font-family:fontawesome-webfont;font-style:normal;font-weight:normal;line-height:1;text-decoration:inherit}a .icon{display:inline-block;text-decoration:inherit}li .icon{display:inline-block}li .icon-large:before,li .icon-large:before{width:1.875em}ul.icons{list-style-type:none;margin-left:2em;text-indent:-0.8em}ul.icons li .icon{width:0.8em}ul.icons li .icon-large:before,ul.icons li .icon-large:before{vertical-align:baseline}.icon-book:before{content:"\f02d"}.icon-caret-down:before{content:"\f0d7"}.icon-caret-up:before{content:"\f0d8"}.icon-caret-left:before{content:"\f0d9"}.icon-caret-right:before{content:"\f0da"}.rst-versions{position:fixed;bottom:0;left:0;width:300px;color:#fcfcfc;background:#1f1d1d;border-top:solid 10px #343131;font-family:"Lato","proxima-nova","Helvetica Neue",Arial,sans-serif;z-index:400}.rst-versions a{color:#2980b9;text-decoration:none}.rst-versions .rst-badge-small{display:none}.rst-versions .rst-current-version{padding:12px;background-color:#272525;display:block;text-align:right;font-size:90%;cursor:pointer;color:#27ae60;*zoom:1}.rst-versions .rst-current-version:before,.rst-versions .rst-current-version:after{display:table;content:""}.rst-versions .rst-current-version:after{clear:both}.rst-versions .rst-current-version .icon{color:#fcfcfc}.rst-versions .rst-current-version .icon-book{float:left}.rst-versions .rst-current-version.rst-out-of-date{background-color:#e74c3c;color:#fff}.rst-versions.shift-up .rst-other-versions{display:block}.rst-versions .rst-other-versions{font-size:90%;padding:12px;color:gray;display:none}.rst-versions .rst-other-versions hr{display:block;height:1px;border:0;margin:20px 0;padding:0;border-top:solid 1px #413d3d}.rst-versions .rst-other-versions dd{display:inline-block;margin:0}.rst-versions .rst-other-versions dd a{display:inline-block;padding:6px;color:#fcfcfc}.rst-versions.rst-badge{width:auto;bottom:20px;right:20px;left:auto;border:none;max-width:300px}.rst-versions.rst-badge .icon-book{float:none}.rst-versions.rst-badge.shift-up .rst-current-version{text-align:right}.rst-versions.rst-badge.shift-up .rst-current-version .icon-book{float:left}.rst-versions.rst-badge .rst-current-version{width:auto;height:30px;line-height:30px;padding:0 6px;display:block;text-align:center}@media screen and (max-width: 768px){.rst-versions{width:85%;display:none}.rst-versions.shift{display:block}img{width:100%;height:auto}}
+.fa:before{-webkit-font-smoothing:antialiased}.clearfix{*zoom:1}.clearfix:before,.clearfix:after{display:table;content:""}.clearfix:after{clear:both}@font-face{font-family:FontAwesome;font-weight:normal;font-style:normal;src:url("../font/fontawesome_webfont.eot");src:url("../font/fontawesome_webfont.eot?#iefix") format("embedded-opentype"),url("../font/fontawesome_webfont.woff") format("woff"),url("../font/fontawesome_webfont.ttf") format("truetype"),url("../font/fontawesome_webfont.svg#FontAwesome") format("svg")}.fa:before{display:inline-block;font-family:FontAwesome;font-style:normal;font-weight:normal;line-height:1;text-decoration:inherit}a .fa{display:inline-block;text-decoration:inherit}li .fa{display:inline-block}li .fa-large:before,li .fa-large:before{width:1.875em}ul.fas{list-style-type:none;margin-left:2em;text-indent:-0.8em}ul.fas li .fa{width:0.8em}ul.fas li .fa-large:before,ul.fas li .fa-large:before{vertical-align:baseline}.fa-book:before{content:""}.icon-book:before{content:""}.fa-caret-down:before{content:""}.icon-caret-down:before{content:""}.fa-caret-up:before{content:""}.icon-caret-up:before{content:""}.fa-caret-left:before{content:""}.icon-caret-left:before{content:""}.fa-caret-right:before{content:""}.icon-caret-right:before{content:""}.rst-versions{position:fixed;bottom:0;left:0;width:300px;color:#fcfcfc;background:#1f1d1d;border-top:solid 10px #343131;font-family:"Lato","proxima-nova","Helvetica Neue",Arial,sans-serif;z-index:400}.rst-versions a{color:#2980B9;text-decoration:none}.rst-versions .rst-badge-small{display:none}.rst-versions .rst-current-version{padding:12px;background-color:#272525;display:block;text-align:right;font-size:90%;cursor:pointer;color:#27AE60;*zoom:1}.rst-versions .rst-current-version:before,.rst-versions .rst-current-version:after{display:table;content:""}.rst-versions .rst-current-version:after{clear:both}.rst-versions .rst-current-version .fa{color:#fcfcfc}.rst-versions .rst-current-version .fa-book{float:left}.rst-versions .rst-current-version .icon-book{float:left}.rst-versions .rst-current-version.rst-out-of-date{background-color:#E74C3C;color:#fff}.rst-versions .rst-current-version.rst-active-old-version{background-color:#F1C40F;color:#000}.rst-versions.shift-up .rst-other-versions{display:block}.rst-versions .rst-other-versions{font-size:90%;padding:12px;color:gray;display:none}.rst-versions .rst-other-versions hr{display:block;height:1px;border:0;margin:20px 0;padding:0;border-top:solid 1px #413d3d}.rst-versions .rst-other-versions dd{display:inline-block;margin:0}.rst-versions .rst-other-versions dd a{display:inline-block;padding:6px;color:#fcfcfc}.rst-versions.rst-badge{width:auto;bottom:20px;right:20px;left:auto;border:none;max-width:300px}.rst-versions.rst-badge .icon-book{float:none}.rst-versions.rst-badge .fa-book{float:none}.rst-versions.rst-badge.shift-up .rst-current-version{text-align:right}.rst-versions.rst-badge.shift-up .rst-current-version .fa-book{float:left}.rst-versions.rst-badge.shift-up .rst-current-version .icon-book{float:left}.rst-versions.rst-badge .rst-current-version{width:auto;height:30px;line-height:30px;padding:0 6px;display:block;text-align:center}@media screen and (max-width: 768px){.rst-versions{width:85%;display:none}.rst-versions.shift{display:block}img{width:100%;height:auto}}
+/*# sourceMappingURL=badge_only.css.map */

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

@@ -0,0 +1,7 @@
+{
+"version": 3,
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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

@@ -3,18 +3,16 @@
 Basic usage
 =====================
 
-Spack is implemented as a single command (``spack``) with many
-*subcommands*.  Only a small subset of commands is needed for typical
-usage.
+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 likely want to do with spack is to install some
-software.  Before that, you need to know what's available.  You can
-see available package names either using the :ref:`package-list`, or
-using the commands below.
+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:
 
@@ -43,54 +41,55 @@ To get more information on a particular package from `spack list`, use
 
 .. command-output:: spack info mpich
 
-Most of the information is self-explanatory.  *Safe versions* are
-versions that Spack has a checksum for, and Spack will use the
-checksum to ensure they downloaded without any errors or malicious
-attacks.  :ref:`Dependencies <sec-specs>` and :ref:`virtual
-dependencies <sec-virtual-dependencies>`, are described in more detail
-later.
+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 *more* 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
 
-There are two sections in the output.  *Safe versions* are ones that
-have already been checksummed.  Spack goes a step further, though, and
-also shows you what versions are available out on the web---these are
-*remote versions*.  Spack gets this information by scraping it
-directly from web pages.  Depending on the package, Spack may or may
-not be able to find any remote versions.
+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.
+
+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
 ------------------------------
 
-Now that you know how to list available packages and versions, you're
-ready to start installing things.
-
 .. _spack-install:
 
 ``spack install``
 ~~~~~~~~~~~~~~~~~~~~~
 
 ``spack install`` will install any package shown by ``spack list``.
-To install the latest version of a package, along with all of its
-dependencies, simply give it a package name:
+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 those
-first.  It then fetches the tarball for ``mpileaks``, expands it,
-verifies that it was downloaded without errors, builds it, and
-installs it in its own directory under ``$SPACK_HOME/opt``. You'll see
+If `mpileaks` depends on other packages, Spack will install the
+dependencies first.  It then fetches the ``mpileaks`` tarball, expands
+it, verifies that it was downloaded without errors, builds it, and
+installs it in its own directory under ``$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:
 
@@ -139,11 +138,11 @@ an installation.  Spack is unique in that it can also configure the
 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.  Specs are described in
-detail in :ref:`sec-specs`.
+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:
 

lib/spack/docs/conf.py

@@ -87,7 +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'
@@ -149,7 +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/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.
 

lib/spack/docs/site_configuration.rst

@@ -8,8 +8,9 @@ Site configuration
 Temporary space
 ----------------------------
 
-.. warning:: Temporary space configuration will be moved to configuration files.
-   The instructions 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

lib/spack/env/cc

@@ -86,19 +86,19 @@ done
 #
 command=$(basename "$0")
 case "$command" in
-    cc|gcc|c89|c99|clang)
+    cc|gcc|c89|c99|clang|xlc)
         command="$SPACK_CC"
         language="C"
         ;;
-    c++|CC|g++|clang++)
+    c++|CC|g++|clang++|xlC)
         command="$SPACK_CXX"
         language="C++"
         ;;
-    f77)
+    f77|xlf)
         command="$SPACK_F77"
         language="Fortran 77"
         ;;
-    fc|f90|f95)
+    fc|f90|f95|xlf90)
         command="$SPACK_FC"
         language="Fortran 90"
         ;;
@@ -262,7 +262,7 @@ done
 
 # Include all -L's and prefix/whatever dirs in rpath
 for dir in "${libraries[@]}"; do
-    [ "$dir" != "." ] && rpaths+=("$dir")
+    [[ dir = $SPACK_INSTALL* ]] && rpaths+=("$dir")
 done
 rpaths+=("$SPACK_PREFIX/lib")
 rpaths+=("$SPACK_PREFIX/lib64")

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/llnl/util/filesystem.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
 ##############################################################################
-__all__ = ['set_install_permissions', 'install', 'expand_user', 'working_dir',
-           'touch', 'touchp', 'mkdirp', 'force_remove', 'join_path', 'ancestor',
-           'can_access', 'filter_file', 'change_sed_delimiter', 'is_exe']
+__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
@@ -140,12 +141,7 @@ def set_install_permissions(path):
         os.chmod(path, 0644)
 
 
-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)
-
+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
@@ -154,6 +150,24 @@ def install(src, dest):
     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)
@@ -210,6 +224,14 @@ def touchp(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:
@@ -228,3 +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/link_tree.py

@@ -32,88 +32,6 @@
 empty_file_name = '.spack-empty'
 
 
-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)
-
-
-
 class LinkTree(object):
     """Class to create trees of symbolic links from a source directory.
 

lib/spack/spack/build_environment.py

@@ -52,6 +52,7 @@
 SPACK_ENV_PATH         = 'SPACK_ENV_PATH'
 SPACK_DEPENDENCIES     = 'SPACK_DEPENDENCIES'
 SPACK_PREFIX           = 'SPACK_PREFIX'
+SPACK_INSTALL          = 'SPACK_INSTALL'
 SPACK_DEBUG            = 'SPACK_DEBUG'
 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)
@@ -125,6 +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.
@@ -159,15 +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')
@@ -189,18 +199,19 @@ def set_module_variables_for_package(pkg):
     m.std_cmake_args.append('-DCMAKE_INSTALL_RPATH=%s' % ":".join(get_rpaths(pkg)))
 
     # 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.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.rmtree     = shutil.rmtree
-    m.move       = shutil.move
+    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.

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/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.")
@@ -54,13 +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,
-                           fake=args.fake)
+        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/spec.py

@@ -33,20 +33,27 @@
 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/compilers/__init__.py

@@ -45,7 +45,7 @@
 _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/fetch_strategy.py

@@ -363,10 +363,6 @@ 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):
@@ -422,6 +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')

lib/spack/spack/package.py

@@ -62,6 +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"]
@@ -332,6 +333,9 @@ class SomePackage(Package):
     """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
 
@@ -477,6 +481,12 @@ def stage(self):
         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:
@@ -780,9 +790,13 @@ def do_install(self, **kwargs):
         """
         # 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)
+        keep_stage   = kwargs.get('keep_stage',  False)
         ignore_deps  = kwargs.get('ignore_deps', False)
-        fake_install = kwargs.get('fake', 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.")
@@ -798,13 +812,26 @@ def do_install(self, **kwargs):
 
         start_time = time.time()
         if not fake_install:
-            self.do_patch()
+            if not skip_patch:
+                self.do_patch()
+            else:
+                self.do_stage()
 
         # 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)
 
+        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)
@@ -837,15 +864,20 @@ def real_work():
                         % (_hms(self._fetch_time), _hms(build_time), _hms(self._total_time)))
                 print_pkg(self.prefix)
 
-            except:
-                if not keep_prefix:
-                    # If anything goes wrong, remove the install prefix
-                    self.remove_prefix()
+            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.warn("Keeping install prefix in place despite error.",
-                             "Spack will think this package is installed." +
-                             "Manually remove this directory to fix:",
-                             self.prefix)
+                    tty.error(e)
+
+                # Still need to clean up b/c there was an error.
+                cleanup()
+
+            except:
+                # other exceptions just clean up and raise.
+                cleanup()
                 raise
 
         build_env.fork(self, real_work)

lib/spack/spack/stage.py

@@ -309,6 +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()

lib/spack/spack/test/git_fetch.py

@@ -109,7 +109,7 @@ def test_fetch_master(self):
         })
 
 
-    def ztest_fetch_branch(self):
+    def test_fetch_branch(self):
         """Test fetching a branch."""
         self.try_fetch(self.repo.branch, self.repo.branch_file, {
             'git'    : self.repo.path,
@@ -117,7 +117,7 @@ def ztest_fetch_branch(self):
         })
 
 
-    def ztest_fetch_tag(self):
+    def test_fetch_tag(self):
         """Test fetching a tag."""
         self.try_fetch(self.repo.tag, self.repo.tag_file, {
             'git' : self.repo.path,
@@ -125,7 +125,7 @@ def ztest_fetch_tag(self):
         })
 
 
-    def ztest_fetch_commit(self):
+    def test_fetch_commit(self):
         """Test fetching a particular commit."""
         self.try_fetch(self.repo.r1, self.repo.r1_file, {
             'git'    : self.repo.path,

lib/spack/spack/util/executable.py

@@ -28,8 +28,10 @@
 import sys
 import re
 import subprocess
+import inspect
 
 import llnl.util.tty as tty
+import spack
 import spack.error
 
 class Executable(object):
@@ -38,6 +40,9 @@ def __init__(self, name):
         self.exe = name.split(' ')
         self.returncode = None
 
+        if not self.exe:
+            raise ProcessError("Cannot construct executable for '%s'" % name)
+
 
     def add_default_arg(self, arg):
         self.exe.append(arg)
@@ -63,7 +68,9 @@ def __call__(self, *args, **kwargs):
                      "Consider removing them")
 
         cmd = self.exe + list(args)
-        tty.debug(" ".join(cmd))
+
+        cmd_line = ' '.join(cmd)
+        tty.debug(cmd_line)
 
         close_error = False
         try:
@@ -79,16 +86,22 @@ def __call__(self, *args, **kwargs):
             self.returncode = proc.returncode
 
             if fail_on_error and proc.returncode != 0:
-                raise ProcessError("command '%s' returned error code %d"
-                                   % (" ".join(cmd), proc.returncode))
+                raise ProcessError("Command exited with status %d:"
+                                   % proc.returncode, cmd_line)
             if return_output:
                 return out
 
+        except OSError, e:
+            raise ProcessError(
+                "%s: %s" % (self.exe[0], e.strerror),
+                "Command: " + cmd_line)
+
         except subprocess.CalledProcessError, e:
             if fail_on_error:
                 raise ProcessError(
-                    "command '%s' failed to run." % (
-                        " ".join(cmd), proc.returncode), str(e))
+                    str(e),
+                    "\nExit status %d when invoking command: %s"
+                    % (proc.returncode, cmd_line))
 
         finally:
             if close_error:
@@ -130,5 +143,27 @@ def which(name, **kwargs):
 
 
 class ProcessError(spack.error.SpackError):
-    def __init__(self, msg, *long_msg):
-        super(ProcessError, self).__init__(msg, *long_msg)
+    def __init__(self, msg, long_msg=None):
+        # Friendlier exception trace info for failed executables
+        long_msg = long_msg + "\n" if long_msg else ""
+        for f in inspect.stack():
+            frame = f[0]
+            loc = frame.f_locals
+            if 'self' in loc:
+                obj = loc['self']
+                if isinstance(obj, spack.Package):
+                    long_msg += "---\n"
+                    long_msg += "Context:\n"
+                    long_msg += "  %s:%d, in %s:\n" % (
+                        inspect.getfile(frame.f_code),
+                        frame.f_lineno,
+                        frame.f_code.co_name)
+
+                    lines, start = inspect.getsourcelines(frame)
+                    for i, line in enumerate(lines):
+                        mark = ">> " if start + i == frame.f_lineno else "   "
+                        long_msg += "  %s%-5d%s\n" % (
+                            mark, start + i, line.rstrip())
+                    break
+
+        super(ProcessError, self).__init__(msg, long_msg)

var/spack/packages/Mitos/package.py

@@ -7,7 +7,7 @@ class Mitos(Package):
     homepage = "https://github.com/scalability-llnl/Mitos"
     url      = "https://github.com/scalability-llnl/Mitos"
 
-    version('0.7', git='https://github.com/scalability-llnl/Mitos.git', tag='v0.7')
+    version('0.7', '319ece59d6794cccb66bfcc0abfec661', git='https://github.com/scalability-llnl/Mitos.git', tag='v0.7')
 
     depends_on('dyninst')
 

var/spack/packages/SAMRAI/package.py

@@ -7,10 +7,11 @@ class Samrai(Package):
        structured adaptive mesh refinement (SAMR) technology in large-scale parallel
        application development.
     """
-    homepage = "https://computation-rnd.llnl.gov/SAMRAI/confirm.php"
-    url      = "https://computation-rnd.llnl.gov/SAMRAI/download/SAMRAI-v3.7.3.tar.gz"
+    homepage = "https://computation.llnl.gov/project/SAMRAI/"
+    url      = "https://computation.llnl.gov/project/SAMRAI/download/SAMRAI-v3.9.1.tar.gz"
     list_url = homepage
 
+    version('3.9.1',      '232d04d0c995f5abf20d94350befd0b2')
     version('3.7.3',      '12d574eacadf8c9a70f1bb4cd1a69df6')
     version('3.7.2',      'f6a716f171c9fdbf3cb12f71fa6e2737')
     version('3.6.3-beta', 'ef0510bf2893042daedaca434e5ec6ce')
@@ -24,22 +25,25 @@ class Samrai(Package):
     depends_on("mpi")
     depends_on("zlib")
     depends_on("hdf5")
-    depends_on("boost@1.52.0")
+    depends_on("boost")
 
     # don't build tools with gcc
     patch('no-tool-build.patch', when='%gcc')
 
     # TODO: currently hard-coded to use openmpi - be careful!
     def install(self, spec, prefix):
+        mpi = next(m for m in ('openmpi', 'mpich', 'mvapich')
+                   if m in spec)
+
         configure(
             "--prefix=%s" % prefix,
-            "--with-CXX=%s" % spec['openmpi'].prefix.bin + "/mpic++",
-            "--with-CC=%s" % spec['openmpi'].prefix.bin + "/mpicc",
+            "--with-CXX=%s" % spec[mpi].prefix.bin + "/mpic++",
+            "--with-CC=%s" % spec[mpi].prefix.bin + "/mpicc",
             "--with-hdf5=%s" % spec['hdf5'].prefix,
             "--with-boost=%s" % spec['boost'].prefix,
             "--with-zlib=%s" % spec['zlib'].prefix,
-            "--disable-blas",
-            "--disable-lapack",
+            "--without-blas",
+            "--without-lapack",
             "--with-hypre=no",
             "--with-petsc=no",
             "--enable-opt",

var/spack/packages/adept-utils/package.py

@@ -30,7 +30,8 @@ class AdeptUtils(Package):
     homepage = "https://github.com/scalability-llnl/adept-utils"
     url      = "https://github.com/scalability-llnl/adept-utils/archive/v1.0.tar.gz"
 
-    version('1.0', '5c6cd9badce56c945ac8551e34804397')
+    version('1.0.1', '731a310717adcb004d9d195130efee7d')
+    version('1.0',   '5c6cd9badce56c945ac8551e34804397')
 
     depends_on("boost")
     depends_on("mpi")

var/spack/packages/binutils/package.py

@@ -0,0 +1,17 @@
+from spack import *
+
+class Binutils(Package):
+    """GNU binutils, which contain the linker, assembler, objdump and others"""
+    homepage = "http://www.gnu.org/software/binutils/"
+    url      = "ftp://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2"
+
+    version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66')
+    version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b')
+    version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e')
+    version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+
+        make()
+        make("install")

var/spack/packages/cppcheck/package.py

@@ -0,0 +1,15 @@
+from spack import *
+
+class Cppcheck(Package):
+    """A tool for static C/C++ code analysis."""
+    homepage = "http://cppcheck.sourceforge.net/"
+    url      = "http://downloads.sourceforge.net/project/cppcheck/cppcheck/1.68/cppcheck-1.68.tar.bz2"
+
+    version('1.68', 'c015195f5d61a542f350269030150708')
+
+    def install(self, spec, prefix):
+        # cppcheck does not have a configure script
+        make()
+        # manually install the final cppcheck binary
+        mkdirp(prefix.bin)
+        install('cppcheck', prefix.bin)

var/spack/packages/cram/package.py

@@ -0,0 +1,15 @@
+from spack import *
+
+class Cram(Package):
+    """Cram runs many small MPI jobs inside one large MPI job."""
+    homepage = "https://github.com/scalability-llnl/cram"
+    url      = "http://github.com/scalability-llnl/cram/archive/v1.0.1.tar.gz"
+
+    version('1.0.1', 'c73711e945cf5dc603e44395f6647f5e')
+
+    depends_on("mpi")
+
+    def install(self, spec, prefix):
+        cmake(".", *std_cmake_args)
+        make()
+        make("install")

var/spack/packages/gcc/package.py

@@ -47,6 +47,7 @@ class Gcc(Package):
     depends_on("gmp")
     depends_on("mpc")     # when @4.5:
     depends_on("libelf")
+    depends_on("binutils")
 
     # Save these until we can do optional deps.
     #depends_on("isl")
@@ -73,6 +74,10 @@ def install(self, spec, prefix):
                   "--with-stage1-ldflags=%s" % self.rpath_args,
                   "--with-boot-ldflags=%s"   % self.rpath_args,
                   "--enable-lto",
+                  "--with-gnu-ld",
+                  "--with-ld=%s/bin/ld" % spec['binutils'].prefix,
+                  "--with-gnu-as",
+                  "--with-as=%s/bin/as" % spec['binutils'].prefix,
                   "--with-quad")
         make()
         make("install")

var/spack/packages/memaxes/package.py

@@ -5,12 +5,11 @@ class Memaxes(Package):
 
     homepage = "https://github.com/scalability-llnl/MemAxes"
 
-    version('0.5', 'b0f561d48aa7301e028d074bc4b5751b',
+    version('0.5', '5874f3fda9fd2d313c0ff9684f915ab5',
             url='https://github.com/scalability-llnl/MemAxes/archive/v0.5.tar.gz')
 
     depends_on("cmake@2.8.9:")
     depends_on("qt@5:")
-    depends_on("vtk")
 
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):

var/spack/packages/metis/package.py

@@ -0,0 +1,32 @@
+from spack import *
+
+class Metis(Package):
+    """METIS is a set of serial programs for partitioning graphs,
+       partitioning finite element meshes, and producing fill reducing
+       orderings for sparse matrices. The algorithms implemented in
+       METIS are based on the multilevel recursive-bisection,
+       multilevel k-way, and multi-constraint partitioning schemes
+       developed in our lab."""
+
+    homepage = "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview"
+    url      = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz"
+
+    version('5.1.0', '5465e67079419a69e0116de24fce58fe')
+
+    # FIXME: Add dependencies if this package requires them.
+    # depends_on("foo")
+
+    def patch(self):
+        filter_file(r'#define IDXTYPEWIDTH 32', '#define IDXTYPEWIDTH 64', 'include/metis.h',
+                    string=True)
+
+
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+            cmake('..',
+                  '-DGKLIB_PATH=../GKlib',
+                  '-DBUILD_SHARED_LIBS=TRUE',
+                  *std_cmake_args)
+            make()
+            make("install")
+

var/spack/packages/mpich/package.py

@@ -38,6 +38,15 @@ class Mpich(Package):
     provides('mpi@:3', when='@3:')
     provides('mpi@:1', when='@1:')
 
+
+    def setup_dependent_environment(self, module, spec, dep_spec):
+        """For dependencies, make mpicc's use spack wrapper."""
+        os.environ['MPICH_CC']  = 'cc'
+        os.environ['MPICH_CXX'] = 'c++'
+        os.environ['MPICH_F77'] = 'f77'
+        os.environ['MPICH_F90'] = 'f90'
+
+
     def install(self, spec, prefix):
         config_args = ["--prefix=" + prefix,
                        "--enable-shared"]

var/spack/packages/muster/package.py

@@ -10,7 +10,8 @@ class Muster(Package):
     homepage = "https://github.com/scalability-llnl/muster"
     url      = "https://github.com/scalability-llnl/muster/archive/v1.0.tar.gz"
 
-    version('1.0', '2eec6979a4a36d3a65a792d12969be16')
+    version('1.0.1', 'd709787db7e080447afb6571ac17723c')
+    version('1.0',   '2eec6979a4a36d3a65a792d12969be16')
 
     depends_on("boost")
     depends_on("mpi")

var/spack/packages/otf/package.py

@@ -0,0 +1,21 @@
+from spack import *
+
+class Otf(Package):
+    """To improve scalability for very large and massively parallel
+       traces the Open Trace Format (OTF) is developed at ZIH as a
+       successor format to the Vampir Trace Format (VTF3)."""
+
+    homepage = "http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/otf/index_html/document_view?set_language=en"
+    url      = "http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.5salmon.tar.gz"
+
+    version('1.12.5salmon', 'bf260198633277031330e3356dcb4eec')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix,
+                  '--without-vtf3',
+                  '--with-zlib',
+                  '--with-zlibsymbols')
+        make()
+        make("install")

var/spack/packages/py-pandas/package.py

@@ -0,0 +1,20 @@
+from spack import *
+import os
+
+class PyPandas(Package):
+    """pandas is a Python package providing fast, flexible, and expressive data structures designed to make working with relational or labeled data both easy and intuitive. It aims to be the fundamental high-level building block for doing practical, real world data analysis in Python. Additionally, it has the broader goal of becoming the most powerful and flexible open source data analysis / manipulation tool available in any language."""
+    homepage = "http://pandas.pydata.org/"
+    url      = "https://pypi.python.org/packages/source/p/pandas/pandas-0.16.0.tar.gz#md5=bfe311f05dc0c351f8955fbd1e296e73"
+
+    version('0.16.0', 'bfe311f05dc0c351f8955fbd1e296e73')
+
+    extends('python')
+    depends_on('py-dateutil')
+    depends_on('py-numpy')
+    depends_on('py-matplotlib')
+    depends_on('py-scipy')
+    depends_on('py-setuptools')
+    depends_on('py-pytz')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/qt/package.py

@@ -50,9 +50,11 @@ def setup_dependent_environment(self, module, spec, dep_spec):
 
     def patch(self):
         if self.spec.satisfies('@4'):
-            qmake_conf = 'mkspecs/common/g++-base.conf'
+            qmake_conf      = 'mkspecs/common/g++-base.conf'
+            qmake_unix_conf = 'mkspecs/common/g++-unix.conf'
         elif self.spec.satisfies('@5'):
-            qmake_conf = 'qtbase/mkspecs/common/g++-base.conf'
+            qmake_conf      = 'qtbase/mkspecs/common/g++-base.conf'
+            qmake_unix_conf = 'qtbase/mkspecs/common/g++-unix.conf'
         else:
             return
 
@@ -60,7 +62,7 @@ def patch(self):
         filter_file(r'^QMAKE_COMPILER *=.*$',  'QMAKE_COMPILER = cc', qmake_conf)
         filter_file(r'^QMAKE_CC *=.*$',        'QMAKE_CC = cc',       qmake_conf)
         filter_file(r'^QMAKE_CXX *=.*$',       'QMAKE_CXX = c++',     qmake_conf)
-
+        filter_file(r'^QMAKE_LFLAGS_NOUNDEF *\+?=.*$',  'QMAKE_LFLAGS_NOUNDEF =', qmake_unix_conf)
 
 
     @property

var/spack/packages/ravel/package.py

@@ -0,0 +1,23 @@
+from spack import *
+
+class Ravel(Package):
+    """Ravel is a parallel communication trace visualization tool that
+       orders events according to logical time."""
+
+    homepage = "https://github.com/scalability-llnl/ravel"
+    url = 'https://github.com/scalability-llnl/ravel/archive/v1.0.0.tar.gz'
+
+    version('1.0.0', 'b25fece58331c2adfcce76c5036485c2')
+
+    # TODO: make this a build dependency
+    depends_on('cmake@2.8.9:')
+
+    depends_on('muster@1.0.1:')
+    depends_on('otf')
+    depends_on('otf2')
+    depends_on('qt@5:')
+
+    def install(self, spec, prefix):
+        cmake('-Wno-dev', *std_cmake_args)
+        make()
+        make("install")

var/spack/packages/scotch/package.py

@@ -0,0 +1,40 @@
+from spack import *
+import glob
+import os
+
+class Scotch(Package):
+    """Scotch is a software package for graph and mesh/hypergraph
+       partitioning, graph clustering, and sparse matrix ordering."""
+    homepage = "http://www.labri.fr/perso/pelegrin/scotch/"
+    url      = "http://gforge.inria.fr/frs/download.php/file/34099/scotch_6.0.3.tar.gz"
+    list_url = "http://gforge.inria.fr/frs/?group_id=248"
+
+    version('6.0.3', '10b0cc0f184de2de99859eafaca83cfc')
+
+    depends_on('mpi')
+
+
+    def patch(self):
+        with working_dir('src/Make.inc'):
+            makefiles = glob.glob('Makefile.inc.x86-64_pc_linux2*')
+            filter_file(r'^CCS\s*=.*$', 'CCS = cc', *makefiles)
+            filter_file(r'^CCD\s*=.*$', 'CCD = cc', *makefiles)
+
+
+    def install(self, spec, prefix):
+        # Currently support gcc and icc on x86_64 (maybe others with
+        # vanilla makefile)
+        makefile = 'Make.inc/Makefile.inc.x86-64_pc_linux2'
+        if spec.satisfies('%icc'):
+            makefile += '.icc'
+
+        with working_dir('src'):
+            force_symlink(makefile, 'Makefile.inc')
+            for app in ('scotch', 'ptscotch'):
+                make(app)
+
+        install_tree('bin', prefix.bin)
+        install_tree('lib', prefix.lib)
+        install_tree('include', prefix.include)
+        install_tree('man/man1', prefix.share_man1)
+

var/spack/packages/uncrustify/package.py

@@ -0,0 +1,14 @@
+from spack import *
+
+class Uncrustify(Package):
+    """Source Code Beautifier for C, C++, C#, ObjectiveC, D, Java, Pawn and VALA"""
+
+    homepage = "http://uncrustify.sourceforge.net/"
+    url      = "http://downloads.sourceforge.net/project/uncrustify/uncrustify/uncrustify-0.61/uncrustify-0.61.tar.gz"
+
+    version('0.61', 'b6140106e74c64e831d0b1c4b6cf7727')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+        make()
+        make("install")