Bootstrap environment-modules

Renames the existing bootstrap command to 'clone'. Repurposes
'spack bootstrap' to install packages that are useful to the
operation of Spack (for now this is just environment-modules).
For bash and ksh users running setup-env.sh, if a Spack-installed
instance of environment-modules is detected and environment modules
and dotkit are not externally available, Spack will define the 
'module' command in the user's shell to use the environment-modules
built by Spack.

4 files changed, 233 insertions, 112 deletions

diff --git a/lib/spack/docs/getting_started.rst b/lib/spack/docs/getting_started.rst
index ef0f25cb04..ffa9bf2414 100644
--- a/lib/spack/docs/getting_started.rst
+++ b/lib/spack/docs/getting_started.rst
@@ -52,7 +52,7 @@ For a richer experience, use Spack's shell support:
 
 .. code-block:: console
 
-   # For bash users
+   # For bash/zsh users
    $ export SPACK_ROOT=/path/to/spack
    $ . $SPACK_ROOT/share/spack/setup-env.sh
 
@@ -60,10 +60,15 @@ For a richer experience, use Spack's shell support:
    $ setenv SPACK_ROOT /path/to/spack
    $ source $SPACK_ROOT/share/spack/setup-env.csh
 
+
 This automatically adds Spack to your ``PATH`` and allows the ``spack``
-command to :ref:`load environment modules <shell-support>` and execute
+command to be used to execute spack :ref:`commands <shell-support>` and
 :ref:`useful packaging commands <packaging-shell-support>`.
 
+If :ref:`environment-modules or dotkit <InstallEnvironmentModules>` is
+installed and available, the ``spack`` command can also load and unload
+:ref:`modules <modules>`.
+
 ^^^^^^^^^^^^^^^^^
 Clean Environment
 ^^^^^^^^^^^^^^^^^
@@ -94,12 +99,12 @@ Optional: Alternate Prefix
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 You may want to run Spack out of a prefix other than the git repository
-you cloned.  The ``spack bootstrap`` command provides this
+you cloned.  The ``spack clone`` command provides this
 functionality.  To install spack in a new directory, simply type:
 
 .. code-block:: console
 
-   $ spack bootstrap /my/favorite/prefix
+   $ spack clone /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
@@ -849,6 +854,10 @@ well.  They can generally be activated as in the ``curl`` example above;
 or some systems might already have an appropriate hand-built
 environment module that may be loaded.  Either way works.
 
+If you find that you are missing some of these programs, ``spack`` can
+build some of them for you with ``spack bootstrap``. Currently supported
+programs are ``environment-modules``.
+
 A few notes on specific programs in this list:
 
 """"""""""""""""""""""""""
@@ -885,52 +894,72 @@ Environment Modules
 In order to use Spack's generated environment modules, you must have
 installed one of *Environment Modules* or *Lmod*.  On many Linux
 distributions, this can be installed from the vendor's repository.  For
-example: ``yum install environment-modules`` (Fedora/RHEL/CentOS).  If
-your Linux distribution does not have Environment Modules, you can get it
-with Spack:
+example: ``yum install environment-modules`` (Fedora/RHEL/CentOS). If
+your Linux distribution does not have Environment Modules, Spack can
+build it for you!
 
-#. Consider using system tcl (as long as your system has Tcl version 8.0 or later):
+What follows are three steps describing how to install and use environment-modules with spack.
 
-   #) Identify its location using ``which tclsh``
-   #) Identify its version using ``echo 'puts $tcl_version;exit 0' | tclsh``
-   #) Add to ``~/.spack/packages.yaml`` and modify as appropriate:
+#. Install ``environment-modules``.
 
-      .. code-block:: yaml
+   * ``spack bootstrap`` will build ``environment-modules`` for you (and may build
+     other packages that are useful to the operation of Spack)
 
-         packages:
-             tcl:
-                 paths:
-                     tcl@8.5: /usr
-                 buildable: False
+   * Install ``environment-modules`` using ``spack install`` with
+     ``spack install environment-modules~X`` (The ``~X`` variant builds without Xorg
+     dependencies, but ``environment-modules`` works fine too.)
 
-#. Install with:
+#. Add ``modulecmd`` to ``PATH`` and create a ``module`` command. 
 
-   .. code-block:: console
+   * If you are using ``bash`` or ``ksh``, Spack can currently do this for you as well.
+     After installing ``environment-modules`` following the step
+     above, source Spack's shell integration script. This will automatically
+     detect the lack of ``modulecmd`` and ``module``, and use the installed
+     ``environment-modules`` from ``spack bootstrap`` or ``spack install``.
+     
+     .. code-block:: console
 
-      $ spack install environment-modules
+        # For bash/zsh users
+        $ export SPACK_ROOT=/path/to/spack
+        $ . $SPACK_ROOT/share/spack/setup-env.sh
 
-#. Activate with the following script (or apply the updates to your
-   ``.bashrc`` file manually):
 
-   .. code-block:: sh
+   * If you prefer to do it manually,  you can activate with the following 
+     script (or apply the updates to your ``.bashrc`` file manually):
 
-      TMP=`tempfile`
-      echo >$TMP
-      MODULE_HOME=`spack location --install-dir environment-modules`
-      MODULE_VERSION=`ls -1 $MODULE_HOME/Modules | head -1`
-      ${MODULE_HOME}/Modules/${MODULE_VERSION}/bin/add.modules <$TMP
-      cp .bashrc $TMP
-      echo "MODULE_VERSION=${MODULE_VERSION}" > .bashrc
-      cat $TMP >>.bashrc
+         .. code-block:: sh
 
-This adds to your ``.bashrc`` (or similar) files, enabling Environment
-Modules when you log in.  Re-load your .bashrc (or log out and in
-again), and then test that the ``module`` command is found with:
+            TMP=`tempfile`
+            echo >$TMP
+            MODULE_HOME=`spack location --install-dir environment-modules`
+            MODULE_VERSION=`ls -1 $MODULE_HOME/Modules | head -1`
+            ${MODULE_HOME}/Modules/${MODULE_VERSION}/bin/add.modules <$TMP
+            cp .bashrc $TMP
+            echo "MODULE_VERSION=${MODULE_VERSION}" > .bashrc
+            cat $TMP >>.bashrc
 
-.. code-block:: console
+      This is added to your ``.bashrc`` (or similar) files, enabling Environment
+      Modules when you log in.
+        
+#. Test that the ``module`` command is found with:
 
-   $ module avail
+   .. code-block:: console
+
+      $ module avail
+
+
+If ``tcl`` 8.0 or later is installed on  your system, you can prevent
+spack from rebuilding ``tcl`` as part of the ``environment-modules`` dependency
+stack by adding the following to your ``~/.spack/packages.yaml`` replacing
+version 8.5 with whatever version is installed on your system:
+
+   .. code-block:: yaml
 
+      packages:
+          tcl:
+              paths:
+                  tcl@8.5: /usr
+              buildable: False
 
 ^^^^^^^^^^^^^^^^^
 Package Utilities
diff --git a/lib/spack/docs/module_file_support.rst b/lib/spack/docs/module_file_support.rst
index 93c2ee33c6..d8f5e561a8 100644
--- a/lib/spack/docs/module_file_support.rst
+++ b/lib/spack/docs/module_file_support.rst
@@ -44,6 +44,7 @@ For ``csh`` and ``tcsh`` instead:
 
    $ source $SPACK_ROOT/share/spack/setup-env.csh
 
+When ``bash`` and ``ksh`` users update their environment with ``setup-env.sh``, it will check for spack-installed environment modules and add the ``module`` command to their environment; This only occurs if the module command is not already available. You can install ``environment-modules`` with ``spack bootstrap`` as described in :ref:`InstallEnvironmentModules`.
 
 .. note::
   You can put the source line in your ``.bashrc`` or ``.cshrc`` to
@@ -54,10 +55,11 @@ For ``csh`` and ``tcsh`` instead:
 Using module files via Spack
 ----------------------------
 
-If you have shell support enabled you should be able to run either
-``module avail`` or ``use -l spack`` to see what module/dotkit files have
-been installed.  Here is sample output of those programs, showing lots
-of installed packages.
+If you have installed a supported module system either manually or through
+``spack bootstrap`` and have enabled shell support, you should be able to
+run either ``module avail`` or ``use -l spack`` to see what module/dotkit
+files have been installed.  Here is sample output of those programs,
+showing lots of installed packages.
 
 .. code-block:: console
 
@@ -210,7 +212,7 @@ Scripts to load modules recursively may be made with the command:
 
     $ spack module loads --dependencies <spec>
 
-An equivalent alternative is:
+An equivalent alternative using `process substitution <http://tldp.org/LDP/abs/html/process-sub.html>`_ is:
 
 .. code-block :: console
 
diff --git a/lib/spack/spack/cmd/bootstrap.py b/lib/spack/spack/cmd/bootstrap.py
index b0550644f8..cd0a21b9e0 100644
--- a/lib/spack/spack/cmd/bootstrap.py
+++ b/lib/spack/spack/cmd/bootstrap.py
@@ -22,86 +22,69 @@
 # 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
-
 import llnl.util.tty as tty
-from llnl.util.filesystem import join_path, mkdirp
-
 import spack
-from spack.util.executable import ProcessError, which
-
-_SPACK_UPSTREAM = 'https://github.com/llnl/spack'
+import spack.cmd
+import spack.cmd.common.arguments as arguments
 
-description = "create a new installation of spack in another prefix"
+description = "Bootstrap packages needed for spack to run smoothly"
 section = "admin"
 level = "long"
 
 
 def setup_parser(subparser):
     subparser.add_argument(
-        '-r', '--remote', action='store', dest='remote',
-        help="name of the remote to bootstrap from", default='origin')
+        '-j', '--jobs', action='store', type=int,
+        help="explicitly set number of make jobs. default is #cpus")
     subparser.add_argument(
-        'prefix',
-        help="names of prefix where we should install spack")
-
-
-def get_origin_info(remote):
-    git_dir = join_path(spack.prefix, '.git')
-    git = which('git', required=True)
-    try:
-        branch = git('symbolic-ref', '--short', 'HEAD', output=str)
-    except ProcessError:
-        branch = 'develop'
-        tty.warn('No branch found; using default branch: %s' % branch)
-    if remote == 'origin' and \
-       branch not in ('master', 'develop'):
-        branch = 'develop'
-        tty.warn('Unknown branch found; using default branch: %s' % branch)
-    try:
-        origin_url = git(
-            '--git-dir=%s' % git_dir,
-            'config', '--get', 'remote.%s.url' % remote,
-            output=str)
-    except ProcessError:
-        origin_url = _SPACK_UPSTREAM
-        tty.warn('No git repository found; '
-                 'using default upstream URL: %s' % origin_url)
-    return (origin_url.strip(), branch.strip())
-
-
-def bootstrap(parser, args):
-    origin_url, branch = get_origin_info(args.remote)
-    prefix = args.prefix
-
-    tty.msg("Fetching spack from '%s': %s" % (args.remote, origin_url))
-
-    if os.path.isfile(prefix):
-        tty.die("There is already a file at %s" % prefix)
-
-    mkdirp(prefix)
-
-    if os.path.exists(join_path(prefix, '.git')):
-        tty.die("There already seems to be a git repository in %s" % prefix)
-
-    files_in_the_way = os.listdir(prefix)
-    if files_in_the_way:
-        tty.die("There are already files there! "
-                "Delete these files before boostrapping spack.",
-                *files_in_the_way)
-
-    tty.msg("Installing:",
-            "%s/bin/spack" % prefix,
-            "%s/lib/spack/..." % prefix)
+        '--keep-prefix', action='store_true', dest='keep_prefix',
+        help="don't remove the install prefix if installation fails")
+    subparser.add_argument(
+        '--keep-stage', action='store_true', dest='keep_stage',
+        help="don't remove the build stage if installation succeeds")
+    subparser.add_argument(
+        '-n', '--no-checksum', action='store_true', dest='no_checksum',
+        help="do not check packages against checksum")
+    subparser.add_argument(
+        '-v', '--verbose', action='store_true', dest='verbose',
+        help="display verbose build output while installing")
 
-    os.chdir(prefix)
-    git = which('git', required=True)
-    git('init', '--shared', '-q')
-    git('remote', 'add', 'origin', origin_url)
-    git('fetch', 'origin', '%s:refs/remotes/origin/%s' % (branch, branch),
-                           '-n', '-q')
-    git('reset', '--hard', 'origin/%s' % branch, '-q')
-    git('checkout', '-B', branch, 'origin/%s' % branch, '-q')
+    cd_group = subparser.add_mutually_exclusive_group()
+    arguments.add_common_arguments(cd_group, ['clean', 'dirty'])
 
-    tty.msg("Successfully created a new spack in %s" % prefix,
-            "Run %s/bin/spack to use this installation." % prefix)
+    subparser.add_argument(
+        '--run-tests', action='store_true', dest='run_tests',
+        help="run package level tests during installation"
+    )
+
+
+def bootstrap(parser, args, **kwargs):
+    kwargs.update({
+        'keep_prefix': args.keep_prefix,
+        'keep_stage': args.keep_stage,
+        'install_deps': 'dependencies',
+        'make_jobs': args.jobs,
+        'run_tests': args.run_tests,
+        'verbose': args.verbose,
+        'dirty': args.dirty
+    })
+
+    # Define requirement dictionary defining general specs which need
+    # to be satisfied, and the specs to install when the general spec
+    # isn't satisfied.
+    requirement_dict = {'environment-modules': 'environment-modules~X'}
+
+    for requirement in requirement_dict:
+        installed_specs = spack.store.db.query(requirement)
+        if(len(installed_specs) > 0):
+            tty.msg("Requirement %s is satisfied with installed "
+                    "package %s" % (requirement, installed_specs[0]))
+        else:
+            # Install requirement
+            spec_to_install = spack.Spec(requirement_dict[requirement])
+            spec_to_install.concretize()
+            tty.msg("Installing %s to satisfy requirement for %s" %
+                    (spec_to_install, requirement))
+            kwargs['explicit'] = True
+            package = spack.repo.get(spec_to_install)
+            package.do_install(**kwargs)
diff --git a/lib/spack/spack/cmd/clone.py b/lib/spack/spack/cmd/clone.py
new file mode 100644
index 0000000000..19201b1f86
--- /dev/null
+++ b/lib/spack/spack/cmd/clone.py
@@ -0,0 +1,107 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import os
+
+import llnl.util.tty as tty
+from llnl.util.filesystem import join_path, mkdirp
+
+import spack
+from spack.util.executable import ProcessError, which
+
+_SPACK_UPSTREAM = 'https://github.com/llnl/spack'
+
+description = "create a new installation of spack in another prefix"
+section = "admin"
+level = "long"
+
+
+def setup_parser(subparser):
+    subparser.add_argument(
+        '-r', '--remote', action='store', dest='remote',
+        help="name of the remote to clone from", default='origin')
+    subparser.add_argument(
+        'prefix',
+        help="names of prefix where we should install spack")
+
+
+def get_origin_info(remote):
+    git_dir = join_path(spack.prefix, '.git')
+    git = which('git', required=True)
+    try:
+        branch = git('symbolic-ref', '--short', 'HEAD', output=str)
+    except ProcessError:
+        branch = 'develop'
+        tty.warn('No branch found; using default branch: %s' % branch)
+    if remote == 'origin' and \
+       branch not in ('master', 'develop'):
+        branch = 'develop'
+        tty.warn('Unknown branch found; using default branch: %s' % branch)
+    try:
+        origin_url = git(
+            '--git-dir=%s' % git_dir,
+            'config', '--get', 'remote.%s.url' % remote,
+            output=str)
+    except ProcessError:
+        origin_url = _SPACK_UPSTREAM
+        tty.warn('No git repository found; '
+                 'using default upstream URL: %s' % origin_url)
+    return (origin_url.strip(), branch.strip())
+
+
+def clone(parser, args):
+    origin_url, branch = get_origin_info(args.remote)
+    prefix = args.prefix
+
+    tty.msg("Fetching spack from '%s': %s" % (args.remote, origin_url))
+
+    if os.path.isfile(prefix):
+        tty.die("There is already a file at %s" % prefix)
+
+    mkdirp(prefix)
+
+    if os.path.exists(join_path(prefix, '.git')):
+        tty.die("There already seems to be a git repository in %s" % prefix)
+
+    files_in_the_way = os.listdir(prefix)
+    if files_in_the_way:
+        tty.die("There are already files there! "
+                "Delete these files before boostrapping spack.",
+                *files_in_the_way)
+
+    tty.msg("Installing:",
+            "%s/bin/spack" % prefix,
+            "%s/lib/spack/..." % prefix)
+
+    os.chdir(prefix)
+    git = which('git', required=True)
+    git('init', '--shared', '-q')
+    git('remote', 'add', 'origin', origin_url)
+    git('fetch', 'origin', '%s:refs/remotes/origin/%s' % (branch, branch),
+                           '-n', '-q')
+    git('reset', '--hard', 'origin/%s' % branch, '-q')
+    git('checkout', '-B', branch, 'origin/%s' % branch, '-q')
+
+    tty.msg("Successfully created a new spack in %s" % prefix,
+            "Run %s/bin/spack to use this installation." % prefix)