Merge branch 'develop' of https://github.com/LLNL/spack into fixes/intel_openmpi

README.md

@@ -19,7 +19,7 @@ written in pure Python, and specs allow package authors to write a
 single build script for many different builds of the same package.
 
 See the
-[Feature Overview](http://llnl.github.io/spack/features.html)
+[Feature Overview](http://software.llnl.gov/spack/features.html)
 for examples and highlights.
 
 To install spack and install your first package:
@@ -31,7 +31,7 @@ To install spack and install your first package:
 Documentation
 ----------------
 
-[**Full documentation**](http://llnl.github.io/spack) for Spack is
+[**Full documentation**](http://software.llnl.gov/spack) for Spack is
 the first place to look.
 
 See also:

bin/sbang

@@ -0,0 +1,84 @@
+#!/bin/bash
+#
+# `sbang`: Run scripts with long shebang lines.
+#
+# Many operating systems limit the length of shebang lines, making it
+# hard to use interpreters that are deep in the directory hierarchy.
+# `sbang` can run such scripts, either as a shebang interpreter, or
+# directly on the command line.
+#
+# Usage
+# -----------------------------
+# Suppose you have a script, long-shebang.sh, like this:
+#
+#     1    #!/very/long/path/to/some/interpreter
+#     2
+#     3    echo "success!"
+#
+# Invoking this script will result in an error on some OS's.  On
+# Linux, you get this:
+#
+#     $ ./long-shebang.sh
+#     -bash: ./long: /very/long/path/to/some/interp: bad interpreter:
+#            No such file or directory
+#
+# On Mac OS X, the system simply assumes the interpreter is the shell
+# and tries to run with it, which is likely not what you want.
+#
+#
+# `sbang` on the command line
+# -----------------------------
+# You can use `sbang` in two ways.  The first is to use it directly,
+# from the command line, like this:
+#
+#     $ sbang ./long-shebang.sh
+#     success!
+#
+#
+# `sbang` as the interpreter
+# -----------------------------
+# You can also use `sbang` *as* the interpreter for your script. Put
+# `#!/bin/bash /path/to/sbang` on line 1, and move the original
+# shebang to line 2 of the script:
+#
+#     1    #!/bin/bash /path/to/sbang
+#     2    #!/long/path/to/real/interpreter with arguments
+#     3
+#     4    echo "success!"
+#
+#     $ ./long-shebang.sh
+#     success!
+#
+# On Linux, you could shorten line 1 to `#!/path/to/sbang`, but other
+# operating systems like Mac OS X require the interpreter to be a
+# binary, so it's best to use `sbang` as a `bash` argument.
+# Obviously, for this to work, `sbang` needs to have a short enough
+# path that *it* will run without hitting OS limits.
+#
+#
+# How it works
+# -----------------------------
+# `sbang` is a very simple bash script. It looks at the first two
+# lines of a script argument and runs the last line starting with
+# `#!`, with the script as an argument. It also forwards arguments.
+#
+
+# First argument is the script we want to actually run.
+script="$1"
+
+# Search the first two lines of script for interpreters.
+lines=0
+while read line && ((lines < 2)) ; do
+    if [[ "$line" = '#!'* ]]; then
+        interpreter="${line#\#!}"
+    fi
+    lines=$((lines+1))
+done < "$script"
+
+# Invoke any interpreter found, or raise an error if none was found.
+if [ -n "$interpreter" ]; then
+    exec $interpreter "$@"
+else
+    echo "error: sbang found no interpreter in $script"
+    exit 1
+fi

lib/spack/docs/basic_usage.rst

@@ -896,7 +896,7 @@ Or, similarly with modules, you could type:
    $ spack load mpich %gcc@4.4.7
 
 These commands will add appropriate directories to your ``PATH``,
-``MANPATH``, and ``LD_LIBRARY_PATH``.  When you no longer want to use
+``MANPATH``, ``CPATH``, and ``LD_LIBRARY_PATH``.  When you no longer want to use
 a package, you can type unload or unuse similarly:
 
 .. code-block:: sh

lib/spack/docs/developer_guide.rst

@@ -73,19 +73,32 @@ with a high level view of Spack's directory structure::
   spack/                  <- installation root
      bin/
         spack             <- main spack executable
+
+     etc/
+        spack/            <- Spack config files.
+                             Can be overridden by files in ~/.spack.
+
      var/
         spack/            <- build & stage directories
+        repos/            <- contains package repositories
+           builtin/       <- pkg repository that comes with Spack
+              repo.yaml   <- descriptor for the builtin repository
+              packages/   <- directories under here contain packages
+
      opt/
         spack/            <- packages are installed here
+
      lib/
         spack/
            docs/          <- source for this documentation
            env/           <- compiler wrappers for build environment
 
+           external/      <- external libs included in Spack distro
+           llnl/          <- some general-use libraries
+
            spack/         <- spack module; contains Python code
               cmd/        <- each file in here is a spack subcommand
               compilers/  <- compiler description files
-              packages/   <- each file in here is a spack package
               test/       <- unit test modules
               util/       <- common code
 

lib/spack/docs/features.rst

@@ -103,7 +103,7 @@ creates a simple python file:
 It doesn't take much python coding to get from there to a working
 package:
 
-.. literalinclude:: ../../../var/spack/packages/libelf/package.py
+.. literalinclude:: ../../../var/spack/repos/builtin/packages/libelf/package.py
    :lines: 25-
 
 Spack also provides wrapper functions around common commands like

lib/spack/docs/getting_started.rst

@@ -22,7 +22,7 @@ go:
    $ spack install libelf
 
 For a richer experience, use Spack's `shell support
-<http://llnl.github.io/spack/basic_usage.html#environment-modules>`_:
+<http://software.llnl.gov/spack/basic_usage.html#environment-modules>`_:
 
 .. code-block:: sh
 

lib/spack/docs/packaging_guide.rst

@@ -84,7 +84,7 @@ always choose to download just one tarball initially, and run
 
    If it fails entirely, you can get minimal boilerplate by using
    :ref:`spack-edit-f`, or you can manually create a directory and
-   ``package.py`` file for the package in ``var/spack/packages``.
+   ``package.py`` file for the package in ``var/spack/repos/builtin/packages``.
 
 .. note::
 
@@ -203,7 +203,7 @@ edit`` command:
 So, if you used ``spack create`` to create a package, then saved and
 closed the resulting file, you can get back to it with ``spack edit``.
 The ``cmake`` package actually lives in
-``$SPACK_ROOT/var/spack/packages/cmake/package.py``, but this provides
+``$SPACK_ROOT/var/spack/repos/builtin/packages/cmake/package.py``, but this provides
 a much simpler shortcut and saves you the trouble of typing the full
 path.
 
@@ -269,18 +269,18 @@ live in Spack's directory structure.  In general, `spack-create`_ and
 `spack-edit`_ handle creating package files for you, so you can skip
 most of the details here.
 
-``var/spack/packages``
+``var/spack/repos/builtin/packages``
 ~~~~~~~~~~~~~~~~~~~~~~~
 
 A Spack installation directory is structured like a standard UNIX
 install prefix (``bin``, ``lib``, ``include``, ``var``, ``opt``,
 etc.).  Most of the code for Spack lives in ``$SPACK_ROOT/lib/spack``.
-Packages themselves live in ``$SPACK_ROOT/var/spack/packages``.
+Packages themselves live in ``$SPACK_ROOT/var/spack/repos/builtin/packages``.
 
 If you ``cd`` to that directory, you will see directories for each
 package:
 
-.. command-output::  cd $SPACK_ROOT/var/spack/packages;  ls -CF
+.. command-output::  cd $SPACK_ROOT/var/spack/repos/builtin/packages;  ls -CF
    :shell:
    :ellipsis: 10
 
@@ -288,7 +288,7 @@ Each directory contains a file called ``package.py``, which is where
 all the python code for the package goes.  For example, the ``libelf``
 package lives in::
 
-   $SPACK_ROOT/var/spack/packages/libelf/package.py
+   $SPACK_ROOT/var/spack/repos/builtin/packages/libelf/package.py
 
 Alongside the ``package.py`` file, a package may contain extra
 directories or files (like patches) that it needs to build.
@@ -301,7 +301,7 @@ Packages are named after the directory containing ``package.py``.  So,
 ``libelf``'s ``package.py`` lives in a directory called ``libelf``.
 The ``package.py`` file defines a class called ``Libelf``, which
 extends Spack's ``Package`` class.  for example, here is
-``$SPACK_ROOT/var/spack/packages/libelf/package.py``:
+``$SPACK_ROOT/var/spack/repos/builtin/packages/libelf/package.py``:
 
 .. code-block:: python
    :linenos:
@@ -328,7 +328,7 @@ these:
    $ spack install libelf@0.8.13
 
 Spack sees the package name in the spec and looks for
-``libelf/package.py`` in ``var/spack/packages``.  Likewise, if you say
+``libelf/package.py`` in ``var/spack/repos/builtin/packages``.  Likewise, if you say
 ``spack install py-numpy``, then Spack looks for
 ``py-numpy/package.py``.
 
@@ -401,6 +401,35 @@ construct the new one for ``8.2.1``.
 When you supply a custom URL for a version, Spack uses that URL
 *verbatim* and does not perform extrapolation.
 
+Skipping the expand step
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Spack normally expands archives automatically after downloading
+them. If you want to skip this step (e.g., for self-extracting
+executables and other custom archive types), you can add
+``expand=False`` to a ``version`` directive.
+
+.. code-block:: python
+
+   version('8.2.1', '4136d7b4c04df68b686570afa26988ac',
+           url='http://example.com/foo-8.2.1-special-version.tar.gz', 'expand=False')
+
+When ``expand`` is set to ``False``, Spack sets the current working
+directory to the directory containing the downloaded archive before it
+calls your ``install`` method.  Within ``install``, the path to the
+downloaded archive is available as ``self.stage.archive_file``.
+
+Here is an example snippet for packages distribuetd as self-extracting
+archives.  The example sets permissions on the downloaded file to make
+it executable, then runs it with some arguments.
+
+.. code-block:: python
+
+   def install(self, spec, prefix):
+       set_executable(self.stage.archive_file)
+       installer = Executable(self.stage.archive_file)
+       installer('--prefix=%s' % prefix, 'arg1', 'arg2', 'etc.')
+
 Checksums
 ~~~~~~~~~~~~~~~~~
 
@@ -703,7 +732,7 @@ supply is a filename, then the patch needs to live within the spack
 source tree.  For example, the patch above lives in a directory
 structure like this::
 
-   $SPACK_ROOT/var/spack/packages/
+   $SPACK_ROOT/var/spack/repos/builtin/packages/
        mvapich2/
            package.py
            ad_lustre_rwcontig_open_source.patch
@@ -1533,7 +1562,7 @@ The last element of a package is its ``install()`` method.  This is
 where the real work of installation happens, and it's the main part of
 the package you'll need to customize for each piece of software.
 
-.. literalinclude::  ../../../var/spack/packages/libelf/package.py
+.. literalinclude::  ../../../var/spack/repos/builtin/packages/libelf/package.py
    :start-after: 0.8.12
    :linenos:
 
@@ -1711,15 +1740,15 @@ Compile-time library search paths
   * ``-L$dep_prefix/lib``
   * ``-L$dep_prefix/lib64``
 Runtime library search paths (RPATHs)
-  * ``-Wl,-rpath=$dep_prefix/lib``
+  * ``-Wl,-rpath,$dep_prefix/lib``
-  * ``-Wl,-rpath=$dep_prefix/lib64``
+  * ``-Wl,-rpath,$dep_prefix/lib64``
 Include search paths
   * ``-I$dep_prefix/include``
 
 An example of this would be the ``libdwarf`` build, which has one
 dependency: ``libelf``.  Every call to ``cc`` in the ``libdwarf``
 build will have ``-I$LIBELF_PREFIX/include``,
-``-L$LIBELF_PREFIX/lib``, and ``-Wl,-rpath=$LIBELF_PREFIX/lib``
+``-L$LIBELF_PREFIX/lib``, and ``-Wl,-rpath,$LIBELF_PREFIX/lib``
 inserted on the command line.  This is done transparently to the
 project's build system, which will just think it's using a system
 where ``libelf`` is readily available.  Because of this, you **do
@@ -2108,6 +2137,15 @@ Filtering functions
 
   Examples:
 
+  #. Filtering a Makefile to force it to use Spack's compiler wrappers:
+
+     .. code-block:: python
+
+        filter_file(r'^CC\s*=.*',  spack_cc,  'Makefile')
+        filter_file(r'^CXX\s*=.*', spack_cxx, 'Makefile')
+        filter_file(r'^F77\s*=.*', spack_f77, 'Makefile')
+        filter_file(r'^FC\s*=.*',  spack_fc,  'Makefile')
+
   #. Replacing ``#!/usr/bin/perl`` with ``#!/usr/bin/env perl`` in ``bib2xhtml``:
 
      .. code-block:: python

lib/spack/env/cc

@@ -90,15 +90,15 @@ case "$command" in
         command="$SPACK_CC"
         language="C"
         ;;
-    c++|CC|g++|clang++|icpc|pgCC|xlc++)
+    c++|CC|g++|clang++|icpc|pgc++|xlc++)
         command="$SPACK_CXX"
         language="C++"
         ;;
-    f90|fc|f95|gfortran|ifort|pgf90|xlf90|nagfor)
+    f90|fc|f95|gfortran|ifort|pgfortran|xlf90|nagfor)
         command="$SPACK_FC"
         language="Fortran 90"
         ;;
-    f77|gfortran|ifort|pgf77|xlf|nagfor)
+    f77|gfortran|ifort|pgfortran|xlf|nagfor)
         command="$SPACK_F77"
         language="Fortran 77"
         ;;
@@ -138,7 +138,7 @@ if [ -z "$mode" ]; then
     done
 fi
 
-# Dump the version and exist if we're in testing mode.
+# Dump the version and exit if we're in testing mode.
 if [ "$SPACK_TEST_COMMAND" = "dump-mode" ]; then
     echo "$mode"
     exit
@@ -187,32 +187,44 @@ while [ -n "$1" ]; do
             ;;
         -Wl,*)
             arg="${1#-Wl,}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
+            # TODO: Handle multiple -Wl, continuations of -Wl,-rpath
-            if [[ "$arg" = -rpath=* ]]; then
+            if [[ $arg == -rpath=* ]]; then
-                rpaths+=("${arg#-rpath=}")
+                arg="${arg#-rpath=}"
-            elif [[ "$arg" = -rpath ]]; then
+                for rpath in ${arg//,/ }; do
+                    rpaths+=("$rpath")
+                done
+            elif [[ $arg == -rpath,* ]]; then
+                arg="${arg#-rpath,}"
+                for rpath in ${arg//,/ }; do
+                    rpaths+=("$rpath")
+                done
+            elif [[ $arg == -rpath ]]; then
                 shift; arg="$1"
-                if [[ "$arg" != -Wl,* ]]; then
+                if [[ $arg != '-Wl,'* ]]; then
                     die "-Wl,-rpath was not followed by -Wl,*"
                 fi
-                rpaths+=("${arg#-Wl,}")
+                arg="${arg#-Wl,}"
+                for rpath in ${arg//,/ }; do
+                    rpaths+=("$rpath")
+                done
             else
                 other_args+=("-Wl,$arg")
             fi
             ;;
-        -Xlinker,*)
+        -Xlinker)
-            arg="${1#-Xlinker,}"
+            shift; arg="$1";
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
+            if [[ $arg = -rpath=* ]]; then
-            if [[ "$arg" = -rpath=* ]]; then
                 rpaths+=("${arg#-rpath=}")
-            elif [[ "$arg" = -rpath ]]; then
+            elif [[ $arg = -rpath ]]; then
                 shift; arg="$1"
-                if [[ "$arg" != -Xlinker,* ]]; then
+                if [[ $arg != -Xlinker ]]; then
-                    die "-Xlinker,-rpath was not followed by -Xlinker,*"
+                    die "-Xlinker -rpath was not followed by -Xlinker <arg>"
                 fi
-                rpaths+=("${arg#-Xlinker,}")
+                shift; arg="$1"
+                rpaths+=("$arg")
             else
-                other_args+=("-Xlinker,$arg")
+                other_args+=("-Xlinker")
+                other_args+=("$arg")
             fi
             ;;
         *)

lib/spack/env/pgi/case-insensitive/pgCC

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

lib/spack/llnl/util/filesystem.py

@@ -25,7 +25,9 @@
 __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',
-           'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink']
+           'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink',
+           'set_executable', 'copy_mode', 'unset_executable_mode',
+           'remove_dead_links', 'remove_linked_tree']
 
 import os
 import sys
@@ -152,15 +154,28 @@ def set_install_permissions(path):
 def copy_mode(src, dest):
     src_mode = os.stat(src).st_mode
     dest_mode = os.stat(dest).st_mode
-    if src_mode | stat.S_IXUSR: dest_mode |= stat.S_IXUSR
+    if src_mode & stat.S_IXUSR: dest_mode |= stat.S_IXUSR
-    if src_mode | stat.S_IXGRP: dest_mode |= stat.S_IXGRP
+    if src_mode & stat.S_IXGRP: dest_mode |= stat.S_IXGRP
-    if src_mode | stat.S_IXOTH: dest_mode |= stat.S_IXOTH
+    if src_mode & stat.S_IXOTH: dest_mode |= stat.S_IXOTH
     os.chmod(dest, dest_mode)
 
 
+def unset_executable_mode(path):
+    mode = os.stat(path).st_mode
+    mode &= ~stat.S_IXUSR
+    mode &= ~stat.S_IXGRP
+    mode &= ~stat.S_IXOTH
+    os.chmod(path, mode)
+
+
 def install(src, dest):
     """Manually install a file to a particular location."""
     tty.debug("Installing %s to %s" % (src, dest))
+
+    # Expand dsst to its eventual full path if it is a directory.
+    if os.path.isdir(dest):
+        dest = join_path(dest, os.path.basename(src))
+
     shutil.copy(src, dest)
     set_install_permissions(dest)
     copy_mode(src, dest)
@@ -235,7 +250,7 @@ def touchp(path):
 def force_symlink(src, dest):
     try:
         os.symlink(src, dest)
-    except OSError, e:
+    except OSError as e:
         os.remove(dest)
         os.symlink(src, dest)
 
@@ -339,3 +354,41 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
 
     if order == 'post':
         yield (source_path, dest_path)
+
+
+def set_executable(path):
+    st = os.stat(path)
+    os.chmod(path, st.st_mode | stat.S_IEXEC)
+
+
+def remove_dead_links(root):
+    """
+    Removes any dead link that is present in root
+
+    Args:
+        root: path where to search for dead links
+
+    """
+    for file in os.listdir(root):
+        path = join_path(root, file)
+        if os.path.islink(path):
+            real_path = os.path.realpath(path)
+            if not os.path.exists(real_path):
+                os.unlink(path)
+
+def remove_linked_tree(path):
+    """
+    Removes a directory and its contents.  If the directory is a
+    symlink, follows the link and removes the real directory before
+    removing the link.
+
+    Args:
+        path: directory to be removed
+
+    """
+    if os.path.exists(path):
+        if os.path.islink(path):
+            shutil.rmtree(os.path.realpath(path), True)
+            os.unlink(path)
+        else:
+            shutil.rmtree(path, True)

lib/spack/spack/build_environment.py

@@ -177,8 +177,6 @@ def set_module_variables_for_package(pkg, m):
     """Populate the module scope of install() with some useful functions.
        This makes things easier for package writers.
     """
-    m = pkg.module
-
     # number of jobs spack will to build with.
     jobs = multiprocessing.cpu_count()
     if not pkg.parallel:
@@ -214,6 +212,13 @@ def set_module_variables_for_package(pkg, m):
     m.std_cmake_args.append('-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE')
     m.std_cmake_args.append('-DCMAKE_INSTALL_RPATH=%s' % ":".join(get_rpaths(pkg)))
 
+    # Put spack compiler paths in module scope.
+    link_dir = spack.build_env_path
+    m.spack_cc  = join_path(link_dir, pkg.compiler.link_paths['cc'])
+    m.spack_cxx = join_path(link_dir, pkg.compiler.link_paths['cxx'])
+    m.spack_f77 = join_path(link_dir, pkg.compiler.link_paths['f77'])
+    m.spack_f90 = join_path(link_dir, pkg.compiler.link_paths['fc'])
+
     # Emulate some shell commands for convenience
     m.pwd          = os.getcwd
     m.cd           = os.chdir

lib/spack/spack/cmd/checksum.py

@@ -22,16 +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 os
-import re
 import argparse
 import hashlib
-from pprint import pprint
-from subprocess import CalledProcessError
 
 import llnl.util.tty as tty
-from llnl.util.tty.colify import colify
-
 import spack
 import spack.cmd
 import spack.util.crypto
@@ -40,6 +34,7 @@
 
 description = "Checksum available versions of a package."
 
+
 def setup_parser(subparser):
     subparser.add_argument(
         'package', metavar='PACKAGE', help='Package to list versions for')
@@ -58,25 +53,23 @@ def get_checksums(versions, urls, **kwargs):
 
     tty.msg("Downloading...")
     hashes = []
-    for i, (url, version) in enumerate(zip(urls, versions)):
+    i = 0
-        stage = Stage(url)
+    for url, version in zip(urls, versions):
         try:
+            with Stage(url, keep=keep_stage) as stage:
                 stage.fetch()
                 if i == 0 and first_stage_function:
                     first_stage_function(stage)
 
-            hashes.append(
+                hashes.append((version,
-                spack.util.crypto.checksum(hashlib.md5, stage.archive_file))
+                               spack.util.crypto.checksum(hashlib.md5, stage.archive_file)))
-        except FailedDownloadError, e:
+                i += 1
+        except FailedDownloadError as e:
             tty.msg("Failed to fetch %s" % url)
-            continue
+        except Exception as e:
-
+            tty.msg('Something failed on %s, skipping.\n    (%s)' % (url, e))
-        finally:
-            if not keep_stage:
-                stage.destroy()
-
-    return zip(versions, hashes)
 
+    return hashes
 
 
 def checksum(parser, args):
@@ -95,11 +88,11 @@ def checksum(parser, args):
     else:
         versions = pkg.fetch_remote_versions()
         if not versions:
-            tty.die("Could not fetch any versions for %s." % pkg.name)
+            tty.die("Could not fetch any versions for %s" % pkg.name)
 
     sorted_versions = sorted(versions, reverse=True)
 
-    tty.msg("Found %s versions of %s." % (len(versions), pkg.name),
+    tty.msg("Found %s versions of %s" % (len(versions), pkg.name),
             *spack.cmd.elide_list(
                 ["%-10s%s" % (v, versions[v]) for v in sorted_versions]))
     print
@@ -116,7 +109,7 @@ def checksum(parser, args):
         keep_stage=args.keep_stage)
 
     if not version_hashes:
-        tty.die("Could not fetch any versions for %s." % pkg.name)
+        tty.die("Could not fetch any versions for %s" % pkg.name)
 
     version_lines = ["    version('%s', '%s')" % (v, h) for v, h in version_hashes]
     tty.msg("Checksummed new versions of %s:" % pkg.name, *version_lines)

lib/spack/spack/cmd/compiler.py

@@ -96,7 +96,7 @@ def compiler_remove(args):
     compilers = spack.compilers.compilers_for_spec(cspec, scope=args.scope)
 
     if not compilers:
-        tty.die("No compilers match spec %s." % cspec)
+        tty.die("No compilers match spec %s" % cspec)
     elif not args.all and len(compilers) > 1:
         tty.error("Multiple compilers match spec %s. Choose one:" % cspec)
         colify(reversed(sorted([c.spec for c in compilers])), indent=4)
@@ -105,7 +105,7 @@ def compiler_remove(args):
 
     for compiler in compilers:
         spack.compilers.remove_compiler_from_config(compiler.spec, scope=args.scope)
-        tty.msg("Removed compiler %s." % compiler.spec)
+        tty.msg("Removed compiler %s" % compiler.spec)
 
 
 def compiler_info(args):
@@ -114,7 +114,7 @@ def compiler_info(args):
     compilers = spack.compilers.compilers_for_spec(cspec, scope=args.scope)
 
     if not compilers:
-        tty.error("No compilers match spec %s." % cspec)
+        tty.error("No compilers match spec %s" % cspec)
     else:
         for c in compilers:
             print str(c.spec) + ":"

lib/spack/spack/cmd/create.py

@@ -156,7 +156,7 @@ def guess_name_and_version(url, args):
     # Try to deduce name and version of the new package from the URL
     version = spack.url.parse_version(url)
     if not version:
-        tty.die("Couldn't guess a version string from %s." % url)
+        tty.die("Couldn't guess a version string from %s" % url)
 
     # Try to guess a name.  If it doesn't work, allow the user to override.
     if args.alternate_name:
@@ -189,7 +189,7 @@ def find_repository(spec, args):
         try:
             repo = Repo(repo_path)
             if spec.namespace and spec.namespace != repo.namespace:
-                tty.die("Can't create package with namespace %s in repo with namespace %s."
+                tty.die("Can't create package with namespace %s in repo with namespace %s"
                         % (spec.namespace, repo.namespace))
         except RepoError as e:
             tty.die(str(e))
@@ -252,7 +252,7 @@ def create(parser, args):
     name = spec.name  # factors out namespace, if any
     repo = find_repository(spec, args)
 
-    tty.msg("This looks like a URL for %s version %s." % (name, version))
+    tty.msg("This looks like a URL for %s version %s" % (name, version))
     tty.msg("Creating template for package %s" % name)
 
     # Fetch tarballs (prompting user if necessary)
@@ -266,7 +266,7 @@ def create(parser, args):
         keep_stage=args.keep_stage)
 
     if not ver_hash_tuples:
-        tty.die("Could not fetch any tarballs for %s." % name)
+        tty.die("Could not fetch any tarballs for %s" % name)
 
     # Prepend 'py-' to python package names, by convention.
     if guesser.build_system == 'python':
@@ -291,4 +291,4 @@ def create(parser, args):
 
     # If everything checks out, go ahead and edit.
     spack.editor(pkg_path)
-    tty.msg("Created package %s." % pkg_path)
+    tty.msg("Created package %s" % pkg_path)

lib/spack/spack/cmd/diy.py

@@ -45,6 +45,9 @@ def setup_parser(subparser):
     subparser.add_argument(
         '--skip-patch', action='store_true',
         help="Skip patching for the DIY build.")
+    subparser.add_argument(
+        '-q', '--quiet', action='store_true', dest='quiet',
+        help="Do not display verbose build output while installing.")
     subparser.add_argument(
         'spec', nargs=argparse.REMAINDER,
         help="specs to use for install.  Must contain package AND verison.")
@@ -92,4 +95,5 @@ def diy(self, args):
         package.do_install(
             keep_prefix=args.keep_prefix,
             ignore_deps=args.ignore_deps,
+            verbose=not args.quiet,
             keep_stage=True)   # don't remove source dir for DIY.

lib/spack/spack/cmd/md5.py

@@ -22,51 +22,51 @@
 # 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 argparse
 import hashlib
-
+import os
-from contextlib import contextmanager
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import *
-
 import spack.util.crypto
 from spack.stage import Stage, FailedDownloadError
 
 description = "Calculate md5 checksums for files/urls."
 
-@contextmanager
-def stager(url):
-    _cwd = os.getcwd()
-    _stager = Stage(url)
-    try:
-        _stager.fetch()
-        yield _stager
-    except FailedDownloadError:
-        tty.msg("Failed to fetch %s" % url)
-    finally:
-        _stager.destroy()
-        os.chdir(_cwd) # the Stage class changes the current working dir so it has to be restored
 
 def setup_parser(subparser):
     setup_parser.parser = subparser
     subparser.add_argument('files', nargs=argparse.REMAINDER,
                            help="Files to checksum.")
 
+
+def compute_md5_checksum(url):
+    if not os.path.isfile(url):
+        with Stage(url) as stage:
+            stage.fetch()
+            value = spack.util.crypto.checksum(hashlib.md5, stage.archive_file)
+    else:
+        value = spack.util.crypto.checksum(hashlib.md5, url)
+    return value
+
+
 def md5(parser, args):
     if not args.files:
         setup_parser.parser.print_help()
         return 1
 
-    for f in args.files:
+    results = []
-        if not os.path.isfile(f):
+    for url in args.files:
-            with stager(f) as stage:
+        try:
-                checksum = spack.util.crypto.checksum(hashlib.md5, stage.archive_file)
+            checksum = compute_md5_checksum(url)
-                print "%s  %s" % (checksum, f)
+            results.append((checksum, url))
-        else:
+        except FailedDownloadError as e:
-            if not can_access(f):
+            tty.warn("Failed to fetch %s" % url)
-                tty.die("Cannot read file: %s" % f)
+            tty.warn("%s" % e)
+        except IOError as e:
+            tty.warn("Error when reading %s" % url)
+            tty.warn("%s" % e)
 
-            checksum = spack.util.crypto.checksum(hashlib.md5, f)
+    # Dump the MD5s at last without interleaving them with downloads
-            print "%s  %s" % (checksum, f)
+    tty.msg("%d MD5 checksums:" % len(results))
+    for checksum, url in results:
+        print "%s  %s" % (checksum, url)

lib/spack/spack/cmd/mirror.py

@@ -126,7 +126,7 @@ def mirror_remove(args):
 
     old_value = mirrors.pop(name)
     spack.config.update_config('mirrors', mirrors, scope=args.scope)
-    tty.msg("Removed mirror %s with url %s." % (name, old_value))
+    tty.msg("Removed mirror %s with url %s" % (name, old_value))
 
 
 def mirror_list(args):
@@ -203,7 +203,7 @@ def mirror_create(args):
 
     verb = "updated" if existed else "created"
     tty.msg(
-        "Successfully %s mirror in %s." % (verb, directory),
+        "Successfully %s mirror in %s" % (verb, directory),
         "Archive stats:",
         "  %-4d already present"  % p,
         "  %-4d added"            % m,

lib/spack/spack/cmd/module.py

@@ -58,7 +58,7 @@ def module_find(mtype, spec_array):
        should type to use that package's module.
     """
     if mtype not in module_types:
-        tty.die("Invalid module type: '%s'.  Options are %s." % (mtype, comma_or(module_types)))
+        tty.die("Invalid module type: '%s'.  Options are %s" % (mtype, comma_or(module_types)))
 
     specs = spack.cmd.parse_specs(spec_array)
     if len(specs) > 1:
@@ -78,7 +78,7 @@ def module_find(mtype, spec_array):
     mt = module_types[mtype]
     mod = mt(specs[0])
     if not os.path.isfile(mod.file_name):
-        tty.die("No %s module is installed for %s." % (mtype, spec))
+        tty.die("No %s module is installed for %s" % (mtype, spec))
 
     print mod.use_name
 
@@ -94,7 +94,7 @@ def module_refresh():
             shutil.rmtree(cls.path, ignore_errors=False)
         mkdirp(cls.path)
         for spec in specs:
-            tty.debug("   Writing file for %s." % spec)
+            tty.debug("   Writing file for %s" % spec)
             cls(spec).write()
 
 

lib/spack/spack/cmd/repo.py

@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/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
@@ -74,51 +74,7 @@ def setup_parser(subparser):
 
 def repo_create(args):
     """Create a new package repository."""
-    root = canonicalize_path(args.directory)
+    full_path, namespace = create_repo(args.directory, args.namespace)
-    namespace = args.namespace
-
-    if not args.namespace:
-        namespace = os.path.basename(root)
-
-    if not re.match(r'\w[\.\w-]*', namespace):
-        tty.die("'%s' is not a valid namespace." % namespace)
-
-    existed = False
-    if os.path.exists(root):
-        if os.path.isfile(root):
-            tty.die('File %s already exists and is not a directory' % root)
-        elif os.path.isdir(root):
-            if not os.access(root, os.R_OK | os.W_OK):
-                tty.die('Cannot create new repo in %s: cannot access directory.' % root)
-            if os.listdir(root):
-                tty.die('Cannot create new repo in %s: directory is not empty.' % root)
-        existed = True
-
-    full_path = os.path.realpath(root)
-    parent = os.path.dirname(full_path)
-    if not os.access(parent, os.R_OK | os.W_OK):
-        tty.die("Cannot create repository in %s: can't access parent!" % root)
-
-    try:
-        config_path = os.path.join(root, repo_config_name)
-        packages_path = os.path.join(root, packages_dir_name)
-
-        mkdirp(packages_path)
-        with open(config_path, 'w') as config:
-            config.write("repo:\n")
-            config.write("  namespace: '%s'\n" % namespace)
-
-    except (IOError, OSError) as e:
-        tty.die('Failed to create new repository in %s.' % root,
-                "Caused by %s: %s" % (type(e), e))
-
-        # try to clean up.
-        if existed:
-            shutil.rmtree(config_path, ignore_errors=True)
-            shutil.rmtree(packages_path, ignore_errors=True)
-        else:
-            shutil.rmtree(root, ignore_errors=True)
-
     tty.msg("Created repo with namespace '%s'." % namespace)
     tty.msg("To register it with spack, run this command:",
             'spack repo add %s' % full_path)
@@ -133,11 +89,11 @@ def repo_add(args):
 
     # check if the path exists
     if not os.path.exists(canon_path):
-        tty.die("No such file or directory: '%s'." % path)
+        tty.die("No such file or directory: %s" % path)
 
     # Make sure the path is a directory.
     if not os.path.isdir(canon_path):
-        tty.die("Not a Spack repository: '%s'." % path)
+        tty.die("Not a Spack repository: %s" % path)
 
     # Make sure it's actually a spack repository by constructing it.
     repo = Repo(canon_path)
@@ -147,7 +103,7 @@ def repo_add(args):
     if not repos: repos = []
 
     if repo.root in repos or path in repos:
-        tty.die("Repository is already registered with Spack: '%s'" % path)
+        tty.die("Repository is already registered with Spack: %s" % path)
 
     repos.insert(0, canon_path)
     spack.config.update_config('repos', repos, args.scope)
@@ -166,7 +122,7 @@ def repo_remove(args):
         if canon_path == repo_canon_path:
             repos.remove(repo_path)
             spack.config.update_config('repos', repos, args.scope)
-            tty.msg("Removed repository '%s'." % repo_path)
+            tty.msg("Removed repository %s" % repo_path)
             return
 
     # If it is a namespace, remove corresponding repo
@@ -176,13 +132,13 @@ def repo_remove(args):
             if repo.namespace == path_or_namespace:
                 repos.remove(path)
                 spack.config.update_config('repos', repos, args.scope)
-                tty.msg("Removed repository '%s' with namespace %s."
+                tty.msg("Removed repository %s with namespace '%s'."
                         % (repo.root, repo.namespace))
                 return
         except RepoError as e:
             continue
 
-    tty.die("No repository with path or namespace: '%s'"
+    tty.die("No repository with path or namespace: %s"
             % path_or_namespace)
 
 

lib/spack/spack/compiler.py

@@ -256,12 +256,12 @@ def find(cls, *path):
 
 
     def __repr__(self):
-        """Return a string represntation of the compiler toolchain."""
+        """Return a string representation of the compiler toolchain."""
         return self.__str__()
 
 
     def __str__(self):
-        """Return a string represntation of the compiler toolchain."""
+        """Return a string representation of the compiler toolchain."""
         return "%s(%s)" % (
             self.name, '\n     '.join((str(s) for s in (self.cc, self.cxx, self.f77, self.fc))))
 

lib/spack/spack/compilers/pgi.py

@@ -29,28 +29,28 @@ class Pgi(Compiler):
     cc_names = ['pgcc']
 
     # Subclasses use possible names of C++ compiler
-    cxx_names = ['pgCC']
+    cxx_names = ['pgc++', 'pgCC']
 
     # Subclasses use possible names of Fortran 77 compiler
-    f77_names = ['pgf77']
+    f77_names = ['pgfortran', 'pgf77']
 
     # Subclasses use possible names of Fortran 90 compiler
-    fc_names = ['pgf95', 'pgf90']
+    fc_names = ['pgfortran', 'pgf95', 'pgf90']
 
     # Named wrapper links within spack.build_env_path
     link_paths = { 'cc'  : 'pgi/pgcc',
-                   'cxx' : 'pgi/case-insensitive/pgCC',
+                   'cxx' : 'pgi/pgc++',
-                   'f77' : 'pgi/pgf77',
+                   'f77' : 'pgi/pgfortran',
-                   'fc'  : 'pgi/pgf90' }
+                   'fc'  : 'pgi/pgfortran' }
 
     @classmethod
     def default_version(cls, comp):
         """The '-V' option works for all the PGI compilers.
            Output looks like this::
 
-               pgf95 10.2-0 64-bit target on x86-64 Linux -tp nehalem-64
+               pgcc 15.10-0 64-bit target on x86-64 Linux -tp sandybridge
-               Copyright 1989-2000, The Portland Group, Inc.  All Rights Reserved.
+               The Portland Group - PGI Compilers and Tools
-               Copyright 2000-2010, STMicroelectronics, Inc.  All Rights Reserved.
+               Copyright (c) 2015, NVIDIA CORPORATION.  All rights reserved.
         """
         return get_compiler_version(
             comp, '-V', r'pg[^ ]* ([^ ]+) \d\d\d?-bit target')

lib/spack/spack/config.py

@@ -205,7 +205,7 @@
 def validate_section_name(section):
     """Raise a ValueError if the section is not a valid section."""
     if section not in section_schemas:
-        raise ValueError("Invalid config section: '%s'.  Options are %s."
+        raise ValueError("Invalid config section: '%s'.  Options are %s"
                          % (section, section_schemas))
 
 
@@ -335,7 +335,7 @@ def validate_scope(scope):
         return config_scopes[scope]
 
     else:
-        raise ValueError("Invalid config scope: '%s'.  Must be one of %s."
+        raise ValueError("Invalid config scope: '%s'.  Must be one of %s"
                          % (scope, config_scopes.keys()))
 
 
@@ -350,7 +350,7 @@ def _read_config_file(filename, schema):
             "Invlaid configuration. %s exists but is not a file." % filename)
 
     elif not os.access(filename, os.R_OK):
-        raise ConfigFileError("Config file is not readable: %s." % filename)
+        raise ConfigFileError("Config file is not readable: %s" % filename)
 
     try:
         tty.debug("Reading config file %s" % filename)

lib/spack/spack/database.py

@@ -330,7 +330,7 @@ def _check_ref_counts(self):
             found = rec.ref_count
             if not expected == found:
                 raise AssertionError(
-                    "Invalid ref_count: %s: %d (expected %d), in DB %s."
+                    "Invalid ref_count: %s: %d (expected %d), in DB %s"
                     % (key, found, expected, self._index_path))
 
 

lib/spack/spack/directives.py

@@ -125,7 +125,7 @@ def __init__(self, dicts=None):
             dicts = (dicts,)
         elif type(dicts) not in (list, tuple):
             raise TypeError(
-                "dicts arg must be list, tuple, or string. Found %s."
+                "dicts arg must be list, tuple, or string. Found %s"
                 % type(dicts))
 
         self.dicts = dicts
@@ -174,7 +174,11 @@ def version(pkg, ver, checksum=None, **kwargs):
 
 
 def _depends_on(pkg, spec, when=None):
-    if when is None:
+    # If when is False do nothing
+    if when is False:
+        return
+    # If when is None or True make sure the condition is always satisfied
+    if when is None or when is True:
         when = pkg.name
     when_spec = parse_anonymous_spec(when, pkg.name)
 
@@ -313,5 +317,5 @@ class CircularReferenceError(DirectiveError):
     def __init__(self, directive, package):
         super(CircularReferenceError, self).__init__(
             directive,
-            "Package '%s' cannot pass itself to %s." % (package, directive))
+            "Package '%s' cannot pass itself to %s" % (package, directive))
         self.package = package

lib/spack/spack/directory_layout.py

@@ -85,6 +85,16 @@ def create_install_directory(self, spec):
         raise NotImplementedError()
 
 
+    def check_installed(self, spec):
+        """Checks whether a spec is installed.
+
+        Return the spec's prefix, if it is installed, None otherwise.
+
+        Raise an exception if the install is inconsistent or corrupt.
+        """
+        raise NotImplementedError()
+
+
     def extension_map(self, spec):
         """Get a dict of currently installed extension packages for a spec.
 
@@ -173,7 +183,9 @@ def __init__(self, root, **kwargs):
 
         self.spec_file_name      = 'spec.yaml'
         self.extension_file_name = 'extensions.yaml'
-        self.build_log_name      = 'build.out' # TODO: use config file.
+        self.build_log_name      = 'build.out'  # build log.
+        self.build_env_name      = 'build.env'  # build environment
+        self.packages_dir        = 'repos'      # archive of package.py files
 
         # Cache of already written/read extension maps.
         self._extension_maps = {}
@@ -231,20 +243,43 @@ def build_log_path(self, spec):
                          self.build_log_name)
 
 
+    def build_env_path(self, spec):
+        return join_path(self.path_for_spec(spec), self.metadata_dir,
+                         self.build_env_name)
+
+
+    def build_packages_path(self, spec):
+        return join_path(self.path_for_spec(spec), self.metadata_dir,
+                         self.packages_dir)
+
+
     def create_install_directory(self, spec):
         _check_concrete(spec)
 
+        prefix = self.check_installed(spec)
+        if prefix:
+            raise InstallDirectoryAlreadyExistsError(prefix)
+
+        mkdirp(self.metadata_path(spec))
+        self.write_spec(spec, self.spec_file_path(spec))
+
+
+    def check_installed(self, spec):
+        _check_concrete(spec)
         path = self.path_for_spec(spec)
         spec_file_path = self.spec_file_path(spec)
 
-        if os.path.isdir(path):
+        if not os.path.isdir(path):
+            return None
+
         if not os.path.isfile(spec_file_path):
             raise InconsistentInstallDirectoryError(
-                    'No spec file found at path %s' % spec_file_path)
+                'Inconsistent state: install prefix exists but contains no spec.yaml:',
+                "  " + path)
 
         installed_spec = self.read_spec(spec_file_path)
-            if installed_spec == self.spec:
+        if installed_spec == spec:
-                raise InstallDirectoryAlreadyExistsError(path)
+            return path
 
         if spec.dag_hash() == installed_spec.dag_hash():
             raise SpecHashCollisionError(installed_hash, spec_hash)
@@ -252,9 +287,6 @@ def create_install_directory(self, spec):
             raise InconsistentInstallDirectoryError(
                 'Spec file in %s does not match hash!' % spec_file_path)
 
-        mkdirp(self.metadata_path(spec))
-        self.write_spec(spec, spec_file_path)
-
 
     def all_specs(self):
         if not os.path.isdir(self.root):
@@ -323,7 +355,7 @@ def _extension_map(self, spec):
 
                         if not dag_hash in by_hash:
                             raise InvalidExtensionSpecError(
-                                "Spec %s not found in %s." % (dag_hash, prefix))
+                                "Spec %s not found in %s" % (dag_hash, prefix))
 
                         ext_spec = by_hash[dag_hash]
                         if not prefix == ext_spec.prefix:
@@ -387,8 +419,8 @@ def remove_extension(self, spec, ext_spec):
 
 class DirectoryLayoutError(SpackError):
     """Superclass for directory layout errors."""
-    def __init__(self, message):
+    def __init__(self, message, long_msg=None):
-        super(DirectoryLayoutError, self).__init__(message)
+        super(DirectoryLayoutError, self).__init__(message, long_msg)
 
 
 class SpecHashCollisionError(DirectoryLayoutError):
@@ -410,8 +442,8 @@ def __init__(self, installed_spec, prefix, error):
 
 class InconsistentInstallDirectoryError(DirectoryLayoutError):
     """Raised when a package seems to be installed to the wrong place."""
-    def __init__(self, message):
+    def __init__(self, message, long_msg=None):
-        super(InconsistentInstallDirectoryError, self).__init__(message)
+        super(InconsistentInstallDirectoryError, self).__init__(message, long_msg)
 
 
 class InstallDirectoryAlreadyExistsError(DirectoryLayoutError):
@@ -438,7 +470,7 @@ class ExtensionConflictError(DirectoryLayoutError):
     """Raised when an extension is added to a package that already has it."""
     def __init__(self, spec, ext_spec, conflict):
         super(ExtensionConflictError, self).__init__(
-            "%s cannot be installed in %s because it conflicts with %s."% (
+            "%s cannot be installed in %s because it conflicts with %s"% (
                 ext_spec.short_spec, spec.short_spec, conflict.short_spec))
 
 

lib/spack/spack/fetch_strategy.py

@@ -82,7 +82,6 @@ class FetchStrategy(object):
 
     class __metaclass__(type):
         """This metaclass registers all fetch strategies in a list."""
-
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
             if cls.enabled: all_strategies.append(cls)
@@ -145,6 +144,8 @@ def __init__(self, url=None, digest=None, **kwargs):
         self.digest = kwargs.get('md5', None)
         if not self.digest: self.digest = digest
 
+        self.expand_archive = kwargs.get('expand', True)
+
         if not self.url:
             raise ValueError("URLFetchStrategy requires a url for fetching.")
 
@@ -153,7 +154,7 @@ def fetch(self):
         self.stage.chdir()
 
         if self.archive_file:
-            tty.msg("Already downloaded %s." % self.archive_file)
+            tty.msg("Already downloaded %s" % self.archive_file)
             return
 
         tty.msg("Trying to fetch from %s" % self.url)
@@ -218,6 +219,10 @@ def archive_file(self):
 
     @_needs_stage
     def expand(self):
+        if not self.expand_archive:
+            tty.msg("Skipping expand step for %s" % self.archive_file)
+            return
+
         tty.msg("Staging archive: %s" % self.archive_file)
 
         self.stage.chdir()
@@ -275,8 +280,8 @@ def check(self):
         checker = crypto.Checker(self.digest)
         if not checker.check(self.archive_file):
             raise ChecksumError(
-                    "%s checksum failed for %s." % (checker.hash_name, self.archive_file),
+                    "%s checksum failed for %s" % (checker.hash_name, self.archive_file),
-                    "Expected %s but got %s." % (self.digest, checker.sum))
+                    "Expected %s but got %s" % (self.digest, checker.sum))
 
     @_needs_stage
     def reset(self):
@@ -312,7 +317,7 @@ def __init__(self, name, *rev_types, **kwargs):
         # Ensure that there's only one of the rev_types
         if sum(k in kwargs for k in rev_types) > 1:
             raise FetchStrategyError(
-                    "Supply only one of %s to fetch with %s." % (
+                    "Supply only one of %s to fetch with %s" % (
                         comma_or(rev_types), name))
 
         # Set attributes for each rev type.
@@ -321,7 +326,7 @@ def __init__(self, name, *rev_types, **kwargs):
 
     @_needs_stage
     def check(self):
-        tty.msg("No checksum needed when fetching with %s." % self.name)
+        tty.msg("No checksum needed when fetching with %s" % self.name)
 
     @_needs_stage
     def expand(self):
@@ -395,7 +400,7 @@ def fetch(self):
         self.stage.chdir()
 
         if self.stage.source_path:
-            tty.msg("Already fetched %s." % self.stage.source_path)
+            tty.msg("Already fetched %s" % self.stage.source_path)
             return
 
         args = []
@@ -505,7 +510,7 @@ def fetch(self):
         self.stage.chdir()
 
         if self.stage.source_path:
-            tty.msg("Already fetched %s." % self.stage.source_path)
+            tty.msg("Already fetched %s" % self.stage.source_path)
             return
 
         tty.msg("Trying to check out svn repository: %s" % self.url)
@@ -584,7 +589,7 @@ def fetch(self):
         self.stage.chdir()
 
         if self.stage.source_path:
-            tty.msg("Already fetched %s." % self.stage.source_path)
+            tty.msg("Already fetched %s" % self.stage.source_path)
             return
 
         args = []

lib/spack/spack/hooks/sbang.py

@@ -0,0 +1,77 @@
+##############################################################################
+# Copyright (c) 2013-2015, 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://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import os
+
+from llnl.util.filesystem import *
+import llnl.util.tty as tty
+
+import spack
+import spack.modules
+
+# Character limit for shebang line.  Using Linux's 127 characters
+# here, as it is the shortest I could find on a modern OS.
+shebang_limit = 127
+
+def shebang_too_long(path):
+    """Detects whether an file has a shebang line that is too long."""
+    with open(path, 'r') as script:
+        bytes = script.read(2)
+        if bytes != '#!':
+            return False
+
+        line = bytes + script.readline()
+        return len(line) > shebang_limit
+
+
+def filter_shebang(path):
+    """Adds a second shebang line, using sbang, at the beginning of a file."""
+    backup = path + ".shebang.bak"
+    os.rename(path, backup)
+
+    with open(backup, 'r') as bak_file:
+        original = bak_file.read()
+
+    with open(path, 'w') as new_file:
+        new_file.write('#!/bin/bash %s/bin/sbang\n' % spack.spack_root)
+        new_file.write(original)
+
+    copy_mode(backup, path)
+    unset_executable_mode(backup)
+
+    tty.warn("Patched overly long shebang in %s" % path)
+
+
+def post_install(pkg):
+    """This hook edits scripts so that they call /bin/bash
+       $spack_prefix/bin/sbang instead of something longer than the
+       shebang limit."""
+    if not os.path.isdir(pkg.prefix.bin):
+        return
+
+    for file in os.listdir(pkg.prefix.bin):
+        path = os.path.join(pkg.prefix.bin, file)
+        if shebang_too_long(path):
+            filter_shebang(path)
+

lib/spack/spack/mirror.py

@@ -51,13 +51,20 @@ def mirror_archive_filename(spec, fetcher):
         raise ValueError("mirror.path requires spec with concrete version.")
 
     if isinstance(fetcher, fs.URLFetchStrategy):
+        if fetcher.expand_archive:
             # If we fetch this version with a URLFetchStrategy, use URL's archive type
             ext = url.downloaded_file_extension(fetcher.url)
+        else:
+            # If the archive shouldn't be expanded, don't check for its extension.
+            ext = None
     else:
         # Otherwise we'll make a .tar.gz ourselves
         ext = 'tar.gz'
 
-    return "%s-%s.%s" % (spec.package.name, spec.version, ext)
+    filename = "%s-%s" % (spec.package.name, spec.version)
+    if ext:
+        filename += ".%s" % ext
+    return filename
 
 
 def mirror_archive_path(spec, fetcher):
@@ -73,7 +80,7 @@ def get_matching_versions(specs, **kwargs):
 
         # Skip any package that has no known versions.
         if not pkg.versions:
-            tty.msg("No safe (checksummed) versions for package %s." % pkg.name)
+            tty.msg("No safe (checksummed) versions for package %s" % pkg.name)
             continue
 
         num_versions = kwargs.get('num_versions', 0)
@@ -110,7 +117,6 @@ def suggest_archive_basename(resource):
     return basename
 
 
-
 def create(path, specs, **kwargs):
     """Create a directory to be used as a spack mirror, and fill it with
        package archives.
@@ -158,17 +164,29 @@ def create(path, specs, **kwargs):
                 "Cannot create directory '%s':" % mirror_root, str(e))
 
     # Things to keep track of while parsing specs.
-    present  = []
+    categories = {
-    mirrored = []
+        'present': [],
-    error    = []
+        'mirrored': [],
+        'error': []
+    }
 
     # Iterate through packages and download all the safe tarballs for each of them
-    everything_already_exists = True
     for spec in version_specs:
-        pkg = spec.package
+        add_single_spec(spec, mirror_root, categories, **kwargs)
+
+    return categories['present'], categories['mirrored'], categories['error']
+
+
+def add_single_spec(spec, mirror_root, categories, **kwargs):
     tty.msg("Adding package {pkg} to mirror".format(pkg=spec.format("$_$@")))
+    spec_exists_in_mirror = True
     try:
-            for ii, stage in enumerate(pkg.stage):
+        with spec.package.stage:
+            # fetcher = stage.fetcher
+            # fetcher.fetch()
+            # ...
+            # fetcher.archive(archive_path)
+            for ii, stage in enumerate(spec.package.stage):
                 fetcher = stage.fetcher
                 if ii == 0:
                     # create a subdirectory for the current package@version
@@ -184,7 +202,7 @@ def create(path, specs, **kwargs):
                 if os.path.exists(archive_path):
                     tty.msg("{name} : already added".format(name=name))
                 else:
-                    everything_already_exists = False
+                    spec_exists_in_mirror = False
                     fetcher.fetch()
                     if not kwargs.get('no_checksum', False):
                         fetcher.check()
@@ -195,20 +213,16 @@ def create(path, specs, **kwargs):
                     fetcher.archive(archive_path)
                     tty.msg("{name} : added".format(name=name))
 
-            if everything_already_exists:
+        if spec_exists_in_mirror:
-                present.append(spec)
+            categories['present'].append(spec)
         else:
-                mirrored.append(spec)
+            categories['mirrored'].append(spec)
-        except Exception, e:
+    except Exception as e:
         if spack.debug:
             sys.excepthook(*sys.exc_info())
         else:
-                tty.warn("Error while fetching %s." % spec.format('$_$@'), e.message)
+            tty.warn("Error while fetching %s" % spec.format('$_$@'), e.message)
-            error.append(spec)
+        categories['error'].append(spec)
-        finally:
-            pkg.stage.destroy()
-
-    return (present, mirrored, error)
 
 
 class MirrorError(spack.error.SpackError):

lib/spack/spack/modules.py

@@ -33,6 +33,7 @@
 
   * /bin directories to be appended to PATH
   * /lib* directories for LD_LIBRARY_PATH
+  * /include directories for CPATH
   * /man* and /share/man* directories for MANPATH
   * the package prefix for CMAKE_PREFIX_PATH
 
@@ -121,6 +122,7 @@ def add_path(path_name, directory):
                     ('LIBRARY_PATH', self.spec.prefix.lib64),
                     ('LD_LIBRARY_PATH', self.spec.prefix.lib),
                     ('LD_LIBRARY_PATH', self.spec.prefix.lib64),
+                    ('CPATH', self.spec.prefix.include),
                     ('PKG_CONFIG_PATH', join_path(self.spec.prefix.lib, 'pkgconfig')),
                     ('PKG_CONFIG_PATH', join_path(self.spec.prefix.lib64, 'pkgconfig'))]:
 

lib/spack/spack/multimethod.py

@@ -138,7 +138,7 @@ class when(object):
        methods like install() that depend on the package's spec.
        For example:
 
-       .. code-block::
+       .. code-block:: python
 
           class SomePackage(Package):
               ...
@@ -163,6 +163,8 @@ def install(self, prefix):
        if you only have part of the install that is platform specific, you
        could do this:
 
+       .. code-block:: python
+
           class SomePackage(Package):
               ...
               # virtual dependence on MPI.
@@ -193,10 +195,11 @@ def install(self, prefix):
        platform-specific versions.  There's not much we can do to get
        around this because of the way decorators work.
     """
-class when(object):
     def __init__(self, spec):
         pkg = get_calling_module_name()
-        self.spec = parse_anonymous_spec(spec, pkg)
+        if spec is True:
+            spec = pkg
+        self.spec = parse_anonymous_spec(spec, pkg) if spec is not False else None
 
     def __call__(self, method):
         # Get the first definition of the method in the calling scope
@@ -207,7 +210,9 @@ def __call__(self, method):
         if not type(original_method) == SpecMultiMethod:
             original_method = SpecMultiMethod(original_method)
 
+        if self.spec is not None:
             original_method.register(self.spec, method)
+
         return original_method
 
 

lib/spack/spack/package.py

@@ -58,6 +58,7 @@
 import spack.mirror
 import spack.hooks
 import spack.directives
+import spack.repository
 import spack.build_environment
 import spack.url
 import spack.util.web
@@ -66,6 +67,7 @@
 from spack.stage import Stage, ResourceStage, StageComposite
 from spack.util.compression import allowed_archive, extension
 from spack.util.executable import ProcessError
+from spack.util.environment import dump_environment
 
 """Allowed URL schemes for spack packages."""
 _ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"]
@@ -454,7 +456,7 @@ def _make_stage(self):
         # Construct a composite stage on top of the composite FetchStrategy
         composite_fetcher = self.fetcher
         composite_stage = StageComposite()
-        resources = self._get_resources()
+        resources = self._get_needed_resources()
         for ii, fetcher in enumerate(composite_fetcher):
             if ii == 0:
                 # Construct root stage first
@@ -465,6 +467,11 @@ def _make_stage(self):
                 stage = self._make_resource_stage(composite_stage[0], fetcher, resource)
             # Append the item to the composite
             composite_stage.append(stage)
+
+        # Create stage on first access.  Needed because fetch, stage,
+        # patch, and install can be called independently of each
+        # other, so `with self.stage:` in do_install isn't sufficient.
+        composite_stage.create()
         return composite_stage
 
     @property
@@ -483,12 +490,14 @@ def stage(self, stage):
 
 
     def _make_fetcher(self):
-        # Construct a composite fetcher that always contains at least one element (the root package). In case there
+        # Construct a composite fetcher that always contains at least
-        # are resources associated with the package, append their fetcher to the composite.
+        # one element (the root package). In case there are resources
+        # associated with the package, append their fetcher to the
+        # composite.
         root_fetcher = fs.for_package_version(self, self.version)
         fetcher = fs.FetchStrategyComposite()  # Composite fetcher
         fetcher.append(root_fetcher)  # Root fetcher is always present
-        resources = self._get_resources()
+        resources = self._get_needed_resources()
         for resource in resources:
             fetcher.append(resource.fetcher)
         return fetcher
@@ -685,7 +694,7 @@ def do_fetch(self, mirror_only=False):
 
             if not ignore_checksum:
                 raise FetchError(
-                    "Will not fetch %s." % self.spec.format('$_$@'), checksum_msg)
+                    "Will not fetch %s" % self.spec.format('$_$@'), checksum_msg)
 
         self.stage.fetch(mirror_only)
 
@@ -705,6 +714,7 @@ def do_stage(self, mirror_only=False):
         self.stage.expand_archive()
         self.stage.chdir_to_source()
 
+
     def do_patch(self):
         """Calls do_stage(), then applied patches to the expanded tarball if they
            haven't been applied already."""
@@ -719,7 +729,7 @@ def do_patch(self):
 
         # If there are no patches, note it.
         if not self.patches and not has_patch_fun:
-            tty.msg("No patches needed for %s." % self.name)
+            tty.msg("No patches needed for %s" % self.name)
             return
 
         # Construct paths to special files in the archive dir used to
@@ -742,7 +752,7 @@ def do_patch(self):
             tty.msg("Already patched %s" % self.name)
             return
         elif os.path.isfile(no_patches_file):
-            tty.msg("No patches needed for %s." % self.name)
+            tty.msg("No patches needed for %s" % self.name)
             return
 
         # Apply all the patches for specs that match this one
@@ -763,10 +773,10 @@ def do_patch(self):
         if has_patch_fun:
             try:
                 self.patch()
-                tty.msg("Ran patch() for %s." % self.name)
+                tty.msg("Ran patch() for %s" % self.name)
                 patched = True
             except:
-                tty.msg("patch() function failed for %s." % self.name)
+                tty.msg("patch() function failed for %s" % self.name)
                 touch(bad_file)
                 raise
 
@@ -797,7 +807,7 @@ def do_fake_install(self):
         mkdirp(self.prefix.man1)
 
 
-    def _get_resources(self):
+    def _get_needed_resources(self):
         resources = []
         # Select the resources that are needed for this build
         for when_spec, resource_list in self.resources.items():
@@ -815,7 +825,7 @@ def _resource_stage(self, resource):
 
 
     def do_install(self,
-                   keep_prefix=False,  keep_stage=False, ignore_deps=False,
+                   keep_prefix=False,  keep_stage=None, ignore_deps=False,
                    skip_patch=False, verbose=False, make_jobs=None, fake=False):
         """Called by commands to install a package and its dependencies.
 
@@ -824,7 +834,8 @@ def do_install(self,
 
         Args:
         keep_prefix -- Keep install prefix on failure. By default, destroys it.
-        keep_stage  -- Keep stage on successful build. By default, destroys it.
+        keep_stage  -- Set to True or false to always keep or always delete stage.
+                       By default, stage is destroyed only if there are no exceptions.
         ignore_deps -- Do not install dependencies before installing this package.
         fake        -- Don't really build -- install fake stub files instead.
         skip_patch  -- Skip patch stage of build if True.
@@ -834,18 +845,26 @@ def do_install(self,
         if not self.spec.concrete:
             raise ValueError("Can only install concrete packages.")
 
-        if os.path.exists(self.prefix):
+        # Ensure package is not already installed
-            tty.msg("%s is already installed in %s." % (self.name, self.prefix))
+        if spack.install_layout.check_installed(self.spec):
+            tty.msg("%s is already installed in %s" % (self.name, self.prefix))
             return
 
         tty.msg("Installing %s" % self.name)
 
+        # First, install dependencies recursively.
         if not ignore_deps:
             self.do_install_dependencies(
                 keep_prefix=keep_prefix, keep_stage=keep_stage, ignore_deps=ignore_deps,
-                fake=fake, skip_patch=skip_patch, verbose=verbose,
+                fake=fake, skip_patch=skip_patch, verbose=verbose, make_jobs=make_jobs)
-                make_jobs=make_jobs)
 
+        # Set parallelism before starting build.
+        self.make_jobs = make_jobs
+
+        # Then install the package itself.
+        def build_process():
+            """Forked for each build. Has its own process and python
+               module space set up by build_environment.fork()."""
             start_time = time.time()
             if not fake:
                 if not skip_patch:
@@ -853,81 +872,72 @@ def do_install(self,
                 else:
                     self.do_stage()
 
-        # create the install directory.  The install layout
+            tty.msg("Building %s" % self.name)
-        # handles this in case so that it can use whatever
-        # package naming scheme it likes.
-        spack.install_layout.create_install_directory(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, wrap=True)
-
-
-        def real_work():
-            try:
-                tty.msg("Building %s." % self.name)
 
+            self.stage.keep = keep_stage
+            with self.stage:
                 # Run the pre-install hook in the child process after
                 # the directory is created.
                 spack.hooks.pre_install(self)
 
-                # Set up process's build environment before running install.
                 if fake:
                     self.do_fake_install()
                 else:
                     # Do the real install in the source directory.
                      self.stage.chdir_to_source()
 
-                    # This redirects I/O to a build log (and optionally to the terminal)
+                     # Save the build environment in a file before building.
+                     env_path = join_path(os.getcwd(), 'spack-build.env')
+
+                     try:
+                        # Redirect I/O to a build log (and optionally to the terminal)
                         log_path = join_path(os.getcwd(), 'spack-build.out')
                         log_file = open(log_path, 'w')
                         with log_output(log_file, verbose, sys.stdout.isatty(), True):
+                            dump_environment(env_path)
                             self.install(self.spec, self.prefix)
 
+                     except ProcessError as e:
+                         # Annotate ProcessErrors with the location of the build log.
+                         e.build_log = log_path
+                         raise e
+
                      # Ensure that something was actually installed.
                      self._sanity_check_install()
 
-                # Move build log into install directory on success
+                     # Copy provenance into the install directory on success
-                if not fake:
                      log_install_path = spack.install_layout.build_log_path(self.spec)
-                    install(log_path, log_install_path)
+                     env_install_path = spack.install_layout.build_env_path(self.spec)
+                     packages_dir = spack.install_layout.build_packages_path(self.spec)
 
-                # On successful install, remove the stage.
+                     install(log_path, log_install_path)
-                if not keep_stage:
+                     install(env_path, env_install_path)
-                    self.stage.destroy()
+                     dump_packages(self.spec, packages_dir)
 
             # Stop timer.
             self._total_time = time.time() - start_time
             build_time = self._total_time - self._fetch_time
 
-                tty.msg("Successfully installed %s." % self.name,
+            tty.msg("Successfully installed %s" % self.name,
                     "Fetch: %s.  Build: %s.  Total: %s."
                     % (_hms(self._fetch_time), _hms(build_time), _hms(self._total_time)))
             print_pkg(self.prefix)
 
-            except ProcessError, e:
+        try:
-                # Annotate with location of build log.
+            # Create the install prefix and fork the build process.
-                e.build_log = log_path
+            spack.install_layout.create_install_directory(self.spec)
-                cleanup()
+            spack.build_environment.fork(self, build_process)
-                raise e
-
         except:
-                # other exceptions just clean up and raise.
+            # remove the install prefix if anything went wrong during install.
-                cleanup()
+            if not keep_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, wrap=True)
             raise
 
-        # Set parallelism before starting build.
-        self.make_jobs = make_jobs
-
-        # Do the build.
-        spack.build_environment.fork(self, real_work)
-
         # note: PARENT of the build process adds the new package to
         # the database, so that we don't need to re-read from file.
         spack.installed_db.add(self.spec, self.prefix)
@@ -1013,7 +1023,7 @@ def do_uninstall(self, force=False):
         # Uninstalling in Spack only requires removing the prefix.
         self.remove_prefix()
         spack.installed_db.remove(self.spec)
-        tty.msg("Successfully uninstalled %s." % self.spec.short_spec)
+        tty.msg("Successfully uninstalled %s" % self.spec.short_spec)
 
         # Once everything else is done, run post install hooks
         spack.hooks.post_uninstall(self)
@@ -1060,7 +1070,7 @@ def do_activate(self, force=False):
         self.extendee_spec.package.activate(self, **self.extendee_args)
 
         spack.install_layout.add_extension(self.extendee_spec, self.spec)
-        tty.msg("Activated extension %s for %s."
+        tty.msg("Activated extension %s for %s"
                 % (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
 
 
@@ -1112,7 +1122,7 @@ def do_deactivate(self, **kwargs):
         if self.activated:
             spack.install_layout.remove_extension(self.extendee_spec, self.spec)
 
-        tty.msg("Deactivated extension %s for %s."
+        tty.msg("Deactivated extension %s for %s"
                 % (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
 
 
@@ -1140,7 +1150,6 @@ def do_restage(self):
 
     def do_clean(self):
         """Removes the package's build stage and source tarball."""
-        if os.path.exists(self.stage.path):
         self.stage.destroy()
 
 
@@ -1180,7 +1189,7 @@ def fetch_remote_versions(self):
         try:
             return spack.util.web.find_versions_of_archive(
                 *self.all_urls, list_url=self.list_url, list_depth=self.list_depth)
-        except spack.error.NoNetworkConnectionError, e:
+        except spack.error.NoNetworkConnectionError as e:
             tty.die("Package.fetch_versions couldn't connect to:",
                     e.url, e.message)
 
@@ -1198,8 +1207,8 @@ def rpath(self):
 
     @property
     def rpath_args(self):
-        """Get the rpath args as a string, with -Wl,-rpath= for each element."""
+        """Get the rpath args as a string, with -Wl,-rpath, for each element."""
-        return " ".join("-Wl,-rpath=%s" % p for p in self.rpath)
+        return " ".join("-Wl,-rpath,%s" % p for p in self.rpath)
 
 
 def validate_package_url(url_string):
@@ -1212,6 +1221,52 @@ def validate_package_url(url_string):
         tty.die("Invalid file type in URL: '%s'" % url_string)
 
 
+def dump_packages(spec, path):
+    """Dump all package information for a spec and its dependencies.
+
+       This creates a package repository within path for every
+       namespace in the spec DAG, and fills the repos wtih package
+       files and patch files for every node in the DAG.
+    """
+    mkdirp(path)
+
+    # Copy in package.py files from any dependencies.
+    # Note that we copy them in as they are in the *install* directory
+    # NOT as they are in the repository, because we want a snapshot of
+    # how *this* particular build was done.
+    for node in spec.traverse():
+        if node is not spec:
+            # Locate the dependency package in the install tree and find
+            # its provenance information.
+            source = spack.install_layout.build_packages_path(node)
+            source_repo_root = join_path(source, node.namespace)
+
+            # There's no provenance installed for the source package.  Skip it.
+            # User can always get something current from the builtin repo.
+            if not os.path.isdir(source_repo_root):
+                continue
+
+            # Create a source repo and get the pkg directory out of it.
+            try:
+                source_repo = spack.repository.Repo(source_repo_root)
+                source_pkg_dir = source_repo.dirname_for_package_name(node.name)
+            except RepoError as e:
+                tty.warn("Warning: Couldn't copy in provenance for %s" % node.name)
+
+        # Create a destination repository
+        dest_repo_root = join_path(path, node.namespace)
+        if not os.path.exists(dest_repo_root):
+            spack.repository.create_repo(dest_repo_root)
+        repo = spack.repository.Repo(dest_repo_root)
+
+        # Get the location of the package in the dest repo.
+        dest_pkg_dir = repo.dirname_for_package_name(node.name)
+        if node is not spec:
+            install_tree(source_pkg_dir, dest_pkg_dir)
+        else:
+            spack.repo.dump_provenance(node, dest_pkg_dir)
+
+
 def print_pkg(message):
     """Outputs a message with a package icon."""
     from llnl.util.tty.color import cwrite
@@ -1262,7 +1317,7 @@ class PackageVersionError(PackageError):
     """Raised when a version URL cannot automatically be determined."""
     def __init__(self, version):
         super(PackageVersionError, self).__init__(
-            "Cannot determine a URL automatically for version %s." % version,
+            "Cannot determine a URL automatically for version %s" % version,
             "Please provide a url for this version in the package.py file.")
 
 

lib/spack/spack/repository.py

@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/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
@@ -33,7 +33,7 @@
 from external import yaml
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import join_path
+from llnl.util.filesystem import *
 
 import spack.error
 import spack.config
@@ -156,7 +156,7 @@ def _add(self, repo):
 
         if repo.namespace in self.by_namespace:
             raise DuplicateRepoError(
-                "Package repos '%s' and '%s' both provide namespace %s."
+                "Package repos '%s' and '%s' both provide namespace %s"
                 % (repo.root, self.by_namespace[repo.namespace].root, repo.namespace))
 
         # Add repo to the pkg indexes
@@ -316,6 +316,16 @@ def get(self, spec, new=False):
         return self.repo_for_pkg(spec).get(spec)
 
 
+    @_autospec
+    def dump_provenance(self, spec, path):
+        """Dump provenance information for a spec to a particular path.
+
+           This dumps the package file and any associated patch files.
+           Raises UnknownPackageError if not found.
+        """
+        return self.repo_for_pkg(spec).dump_provenance(spec, path)
+
+
     def dirname_for_package_name(self, pkg_name):
         return self.repo_for_pkg(pkg_name).dirname_for_package_name(pkg_name)
 
@@ -535,7 +545,7 @@ def get(self, spec, new=False):
             raise UnknownPackageError(spec.name)
 
         if spec.namespace and spec.namespace != self.namespace:
-            raise UnknownPackageError("Repository %s does not contain package %s."
+            raise UnknownPackageError("Repository %s does not contain package %s"
                                       % (self.namespace, spec.fullname))
 
         key = hash(spec)
@@ -552,6 +562,35 @@ def get(self, spec, new=False):
         return self._instances[key]
 
 
+    @_autospec
+    def dump_provenance(self, spec, path):
+        """Dump provenance information for a spec to a particular path.
+
+           This dumps the package file and any associated patch files.
+           Raises UnknownPackageError if not found.
+        """
+        # Some preliminary checks.
+        if spec.virtual:
+            raise UnknownPackageError(spec.name)
+
+        if spec.namespace and spec.namespace != self.namespace:
+            raise UnknownPackageError("Repository %s does not contain package %s."
+                                      % (self.namespace, spec.fullname))
+
+        # Install any patch files needed by packages.
+        mkdirp(path)
+        for spec, patches in spec.package.patches.items():
+            for patch in patches:
+                if patch.path:
+                    if os.path.exists(patch.path):
+                        install(patch.path, path)
+                    else:
+                        tty.warn("Patch file did not exist: %s" % patch.path)
+
+        # Install the package.py file itself.
+        install(self.filename_for_package_name(spec), path)
+
+
     def purge(self):
         """Clear entire package instance cache."""
         self._instances.clear()
@@ -705,6 +744,58 @@ def __contains__(self, pkg_name):
         return self.exists(pkg_name)
 
 
+def create_repo(root, namespace=None):
+    """Create a new repository in root with the specified namespace.
+
+       If the namespace is not provided, use basename of root.
+       Return the canonicalized path and the namespace of the created repository.
+    """
+    root = canonicalize_path(root)
+    if not namespace:
+        namespace = os.path.basename(root)
+
+    if not re.match(r'\w[\.\w-]*', namespace):
+        raise InvalidNamespaceError("'%s' is not a valid namespace." % namespace)
+
+    existed = False
+    if os.path.exists(root):
+        if os.path.isfile(root):
+            raise BadRepoError('File %s already exists and is not a directory' % root)
+        elif os.path.isdir(root):
+            if not os.access(root, os.R_OK | os.W_OK):
+                raise BadRepoError('Cannot create new repo in %s: cannot access directory.' % root)
+            if os.listdir(root):
+                raise BadRepoError('Cannot create new repo in %s: directory is not empty.' % root)
+        existed = True
+
+    full_path = os.path.realpath(root)
+    parent = os.path.dirname(full_path)
+    if not os.access(parent, os.R_OK | os.W_OK):
+        raise BadRepoError("Cannot create repository in %s: can't access parent!" % root)
+
+    try:
+        config_path = os.path.join(root, repo_config_name)
+        packages_path = os.path.join(root, packages_dir_name)
+
+        mkdirp(packages_path)
+        with open(config_path, 'w') as config:
+            config.write("repo:\n")
+            config.write("  namespace: '%s'\n" % namespace)
+
+    except (IOError, OSError) as e:
+        raise BadRepoError('Failed to create new repository in %s.' % root,
+                           "Caused by %s: %s" % (type(e), e))
+
+        # try to clean up.
+        if existed:
+            shutil.rmtree(config_path, ignore_errors=True)
+            shutil.rmtree(packages_path, ignore_errors=True)
+        else:
+            shutil.rmtree(root, ignore_errors=True)
+
+    return full_path, namespace
+
+
 class RepoError(spack.error.SpackError):
     """Superclass for repository-related errors."""
 
@@ -713,6 +804,10 @@ class NoRepoConfiguredError(RepoError):
     """Raised when there are no repositories configured."""
 
 
+class InvalidNamespaceError(RepoError):
+    """Raised when an invalid namespace is encountered."""
+
+
 class BadRepoError(RepoError):
     """Raised when repo layout is invalid."""
 
@@ -730,7 +825,7 @@ class UnknownPackageError(PackageLoadError):
     def __init__(self, name, repo=None):
         msg = None
         if repo:
-            msg = "Package %s not found in repository %s." % (name, repo)
+            msg = "Package %s not found in repository %s" % (name, repo)
         else:
             msg = "Package %s not found." % name
         super(UnknownPackageError, self).__init__(msg)

lib/spack/spack/resource.py

@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify

lib/spack/spack/stage.py

@@ -42,36 +42,53 @@
 
 
 class Stage(object):
-    """A Stage object manages a directory where some source code is
+    """Manages a temporary stage directory for building.
-       downloaded and built before being installed.  It handles
-       fetching the source code, either as an archive to be expanded
-       or by checking it out of a repository.  A stage's lifecycle
-       looks like this:
 
-       Stage()
+    A Stage object is a context manager that handles a directory where
-         Constructor creates the stage directory.
+    some source code is downloaded and built before being installed.
-       fetch()
+    It handles fetching the source code, either as an archive to be
-         Fetch a source archive into the stage.
+    expanded or by checking it out of a repository.  A stage's
-       expand_archive()
+    lifecycle looks like this:
-         Expand the source archive.
-       <install>
-         Build and install the archive.  This is handled by the Package class.
-       destroy()
-         Remove the stage once the package has been installed.
 
-       If spack.use_tmp_stage is True, spack will attempt to create stages
+    ```
-       in a tmp directory.  Otherwise, stages are created directly in
+    with Stage() as stage:      # Context manager creates and destroys the stage directory
-       spack.stage_path.
+        stage.fetch()           # Fetch a source archive into the stage.
+        stage.expand_archive()  # Expand the source archive.
+        <install>               # Build and install the archive. (handled by user of Stage)
+    ```
 
-       There are two kinds of stages: named and unnamed.  Named stages can
+    When used as a context manager, the stage is automatically
-       persist between runs of spack, e.g. if you fetched a tarball but
+    destroyed if no exception is raised by the context. If an
-       didn't finish building it, you won't have to fetch it again.
+    excpetion is raised, the stage is left in the filesystem and NOT
+    destroyed, for potential reuse later.
+
+    You can also use the stage's create/destroy functions manually,
+    like this:
+
+    ```
+    stage = Stage()
+    try:
+        stage.create()          # Explicitly create the stage directory.
+        stage.fetch()           # Fetch a source archive into the stage.
+        stage.expand_archive()  # Expand the source archive.
+        <install>               # Build and install the archive. (handled by user of Stage)
+    finally:
+        stage.destroy()         # Explicitly destroy the stage directory.
+    ```
+
+    If spack.use_tmp_stage is True, spack will attempt to create
+    stages in a tmp directory.  Otherwise, stages are created directly
+    in spack.stage_path.
+
+    There are two kinds of stages: named and unnamed.  Named stages
+    can persist between runs of spack, e.g. if you fetched a tarball
+    but didn't finish building it, you won't have to fetch it again.
 
     Unnamed stages are created using standard mkdtemp mechanisms or
     similar, and are intended to persist for only one run of spack.
     """
 
-    def __init__(self, url_or_fetch_strategy, **kwargs):
+    def __init__(self, url_or_fetch_strategy, name=None, mirror_path=None, keep=None):
         """Create a stage object.
            Parameters:
              url_or_fetch_strategy
@@ -83,6 +100,18 @@ def __init__(self, url_or_fetch_strategy, **kwargs):
                  and will persist between runs (or if you construct another
                  stage object later).  If name is not provided, then this
                  stage will be given a unique name automatically.
+
+             mirror_path
+                 If provided, Stage will search Spack's mirrors for
+                 this archive at the mirror_path, before using the
+                 default fetch strategy.
+
+             keep
+                 By default, when used as a context manager, the Stage
+                 is cleaned up when everything goes well, and it is
+                 kept intact when an exception is raised. You can
+                 override this behavior by setting keep to True
+                 (always keep) or False (always delete).
         """
         # TODO: fetch/stage coupling needs to be reworked -- the logic
         # TODO: here is convoluted and not modular enough.
@@ -96,21 +125,55 @@ def __init__(self, url_or_fetch_strategy, **kwargs):
         self.default_fetcher = self.fetcher  # self.fetcher can change with mirrors.
         self.skip_checksum_for_mirror = True  # used for mirrored archives of repositories.
 
-        self.name = kwargs.get('name')
+        # TODO : this uses a protected member of tempfile, but seemed the only way to get a temporary name
-        self.mirror_path = kwargs.get('mirror_path')
+        # TODO : besides, the temporary link name won't be the same as the temporary stage area in tmp_root
+        self.name = name
+        if name is None:
+            self.name = STAGE_PREFIX + next(tempfile._get_candidate_names())
+        self.mirror_path = mirror_path
         self.tmp_root = find_tmp_root()
 
-        self.path = None
+        # Try to construct here a temporary name for the stage directory
-        self._setup()
+        # If this is a named stage, then construct a named path.
+        self.path = join_path(spack.stage_path, self.name)
+
+        # Flag to decide whether to delete the stage folder on exit or not
+        self.keep = keep
+
+
+    def __enter__(self):
+        """
+        Entering a stage context will create the stage directory
+
+        Returns:
+            self
+        """
+        self.create()
+        return self
+
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        """
+        Exiting from a stage context will delete the stage directory unless:
+        - it was explicitly requested not to do so
+        - an exception has been raised
+
+        Args:
+            exc_type: exception type
+            exc_val: exception value
+            exc_tb: exception traceback
+
+        Returns:
+            Boolean
+        """
+        if self.keep is None:
+            # Default: delete when there are no exceptions.
+            if exc_type is None: self.destroy()
+
+        elif not self.keep:
+            # Overridden. Either always keep or always delete.
+            self.destroy()
 
-    def _cleanup_dead_links(self):
-        """Remove any dead links in the stage directory."""
-        for file in os.listdir(spack.stage_path):
-            path = join_path(spack.stage_path, file)
-            if os.path.islink(path):
-                real_path = os.path.realpath(path)
-                if not os.path.exists(path):
-                    os.unlink(path)
 
     def _need_to_create_path(self):
         """Makes sure nothing weird has happened since the last time we
@@ -148,54 +211,6 @@ def _need_to_create_path(self):
 
         return False
 
-    def _setup(self):
-        """Creates the stage directory.
-           If spack.use_tmp_stage is False, the stage directory is created
-           directly under spack.stage_path.
-
-           If spack.use_tmp_stage is True, this will attempt to create a
-           stage in a temporary directory and link it into spack.stage_path.
-           Spack will use the first writable location in spack.tmp_dirs to
-           create a stage.  If there is no valid location in tmp_dirs, fall
-           back to making the stage inside spack.stage_path.
-        """
-        # Create the top-level stage directory
-        mkdirp(spack.stage_path)
-        self._cleanup_dead_links()
-
-        # If this is a named stage, then construct a named path.
-        if self.name is not None:
-            self.path = join_path(spack.stage_path, self.name)
-
-        # If this is a temporary stage, them make the temp directory
-        tmp_dir = None
-        if self.tmp_root:
-            if self.name is None:
-                # Unnamed tmp root.  Link the path in
-                tmp_dir = tempfile.mkdtemp('', STAGE_PREFIX, self.tmp_root)
-                self.name = os.path.basename(tmp_dir)
-                self.path = join_path(spack.stage_path, self.name)
-                if self._need_to_create_path():
-                    os.symlink(tmp_dir, self.path)
-
-            else:
-                if self._need_to_create_path():
-                    tmp_dir = tempfile.mkdtemp('', STAGE_PREFIX, self.tmp_root)
-                    os.symlink(tmp_dir, self.path)
-
-        # if we're not using a tmp dir, create the stage directly in the
-        # stage dir, rather than linking to it.
-        else:
-            if self.name is None:
-                self.path = tempfile.mkdtemp('', STAGE_PREFIX, spack.stage_path)
-                self.name = os.path.basename(self.path)
-            else:
-                if self._need_to_create_path():
-                    mkdirp(self.path)
-
-        # Make sure we can actually do something with the stage we made.
-        ensure_access(self.path)
-
     @property
     def archive_file(self):
         """Path to the source archive within this stage directory."""
@@ -214,13 +229,22 @@ def archive_file(self):
 
     @property
     def source_path(self):
-        """Returns the path to the expanded/checked out source code
+        """Returns the path to the expanded/checked out source code.
-           within this fetch strategy's path.
 
-           This assumes nothing else is going ot be put in the
+        To find the source code, this method searches for the first
-           FetchStrategy's path.  It searches for the first
+        subdirectory of the stage that it can find, and returns it.
-           subdirectory of the path it can find, then returns that.
+        This assumes nothing besides the archive file will be in the
+        stage path, but it has the advantage that we don't need to
+        know the name of the archive or its contents.
+
+        If the fetch strategy is not supposed to expand the downloaded
+        file, it will just return the stage path. If the archive needs
+        to be expanded, it will return None when no archive is found.
         """
+        if isinstance(self.fetcher, fs.URLFetchStrategy):
+            if not self.fetcher.expand_archive:
+                return self.path
+
         for p in [os.path.join(self.path, f) for f in os.listdir(self.path)]:
             if os.path.isdir(p):
                 return p
@@ -231,7 +255,7 @@ def chdir(self):
         if os.path.isdir(self.path):
             os.chdir(self.path)
         else:
-            tty.die("Setup failed: no such directory: " + self.path)
+            raise ChdirError("Setup failed: no such directory: " + self.path)
 
     def fetch(self, mirror_only=False):
         """Downloads an archive or checks out code from a repository."""
@@ -276,7 +300,7 @@ def fetch(self, mirror_only=False):
                 self.fetcher = fetcher
                 self.fetcher.fetch()
                 break
-            except spack.error.SpackError, e:
+            except spack.error.SpackError as e:
                 tty.msg("Fetching from %s failed." % fetcher)
                 tty.debug(e)
                 continue
@@ -306,9 +330,9 @@ def expand_archive(self):
         archive_dir = self.source_path
         if not archive_dir:
             self.fetcher.expand()
-            tty.msg("Created stage in %s." % self.path)
+            tty.msg("Created stage in %s" % self.path)
         else:
-            tty.msg("Already staged %s in %s." % (self.name, self.path))
+            tty.msg("Already staged %s in %s" % (self.name, self.path))
 
     def chdir_to_source(self):
         """Changes directory to the expanded archive directory.
@@ -328,8 +352,35 @@ def restage(self):
         """
         self.fetcher.reset()
 
+    def create(self):
+        """
+        Creates the stage directory
+
+        If self.tmp_root evaluates to False, the stage directory is
+        created directly under spack.stage_path, otherwise this will
+        attempt to create a stage in a temporary directory and link it
+        into spack.stage_path.
+
+        Spack will use the first writable location in spack.tmp_dirs
+        to create a stage. If there is no valid location in tmp_dirs,
+        fall back to making the stage inside spack.stage_path.
+        """
+        # Create the top-level stage directory
+        mkdirp(spack.stage_path)
+        remove_dead_links(spack.stage_path)
+        # If a tmp_root exists then create a directory there and then link it in the stage area,
+        # otherwise create the stage directory in self.path
+        if self._need_to_create_path():
+            if self.tmp_root:
+                tmp_dir = tempfile.mkdtemp('', STAGE_PREFIX, self.tmp_root)
+                os.symlink(tmp_dir, self.path)
+            else:
+                mkdirp(self.path)
+        # Make sure we can actually do something with the stage we made.
+        ensure_access(self.path)
+
     def destroy(self):
-        """Remove this stage directory."""
+        """Removes this stage directory."""
         remove_linked_tree(self.path)
 
         # Make sure we don't end up in a removed directory
@@ -374,13 +425,28 @@ def expand_archive(self):
                 shutil.move(source_path, destination_path)
 
 
-@pattern.composite(method_list=['fetch', 'check', 'expand_archive', 'restage', 'destroy'])
+@pattern.composite(method_list=['fetch', 'create', 'check', 'expand_archive',  'restage', 'destroy'])
 class StageComposite:
     """
     Composite for Stage type objects. The first item in this composite is considered to be the root package, and
     operations that return a value are forwarded to it.
     """
+    #
+    # __enter__ and __exit__ delegate to all stages in the composite.
+    #
+    def __enter__(self):
+        for item in self:
+            item.__enter__()
+        return self
 
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        for item in reversed(self):
+            item.keep = getattr(self, 'keep', None)
+            item.__exit__(exc_type, exc_val, exc_tb)
+
+    #
+    # Below functions act only on the *first* stage in the composite.
+    #
     @property
     def source_path(self):
         return self[0].source_path
@@ -392,6 +458,10 @@ def path(self):
     def chdir_to_source(self):
         return self[0].chdir_to_source()
 
+    @property
+    def archive_file(self):
+        return self[0].archive_file
+
 
 class DIYStage(object):
     """Simple class that allows any directory to be a spack stage."""
@@ -405,12 +475,16 @@ def chdir(self):
         if os.path.isdir(self.path):
             os.chdir(self.path)
         else:
-            tty.die("Setup failed: no such directory: " + self.path)
+            raise ChdirError("Setup failed: no such directory: " + self.path)
+
+    # DIY stages do nothing as context managers.
+    def __enter__(self): pass
+    def __exit__(self, exc_type, exc_val, exc_tb): pass
 
     def chdir_to_source(self):
         self.chdir()
 
-    def fetch(self):
+    def fetch(self, mirror_only):
         tty.msg("No need to fetch for DIY.")
 
     def check(self):
@@ -439,19 +513,6 @@ def ensure_access(file=spack.stage_path):
         tty.die("Insufficient permissions for %s" % file)
 
 
-def remove_linked_tree(path):
-    """Removes a directory and its contents.  If the directory is a symlink,
-       follows the link and reamoves the real directory before removing the
-       link.
-    """
-    if os.path.exists(path):
-        if os.path.islink(path):
-            shutil.rmtree(os.path.realpath(path), True)
-            os.unlink(path)
-        else:
-            shutil.rmtree(path, True)
-
-
 def purge():
     """Remove all build directories in the top-level stage path."""
     if os.path.isdir(spack.stage_path):
@@ -480,19 +541,15 @@ def find_tmp_root():
 
 
 class StageError(spack.error.SpackError):
-    def __init__(self, message, long_message=None):
+    """"Superclass for all errors encountered during staging."""
-        super(self, StageError).__init__(message, long_message)
 
 
 class RestageError(StageError):
-    def __init__(self, message, long_msg=None):
+    """"Error encountered during restaging."""
-        super(RestageError, self).__init__(message, long_msg)
 
 
 class ChdirError(StageError):
-    def __init__(self, message, long_msg=None):
+    """Raised when Spack can't change directories."""
-        super(ChdirError, self).__init__(message, long_msg)
-
 
 # Keep this in namespace for convenience
 FailedDownloadError = fs.FailedDownloadError

lib/spack/spack/test/cc.py

@@ -39,11 +39,11 @@
     'arg1',
     '-Wl,--start-group',
     'arg2',
-    '-Wl,-rpath=/first/rpath', 'arg3', '-Wl,-rpath', '-Wl,/second/rpath',
+    '-Wl,-rpath,/first/rpath', 'arg3', '-Wl,-rpath', '-Wl,/second/rpath',
     '-llib1', '-llib2',
     'arg4',
     '-Wl,--end-group',
-    '-Xlinker,-rpath', '-Xlinker,/third/rpath', '-Xlinker,-rpath=/fourth/rpath',
+    '-Xlinker', '-rpath', '-Xlinker', '/third/rpath', '-Xlinker', '-rpath', '-Xlinker', '/fourth/rpath',
     '-llib3', '-llib4',
     'arg5', 'arg6']
 
@@ -95,13 +95,13 @@ def test_cpp_mode(self):
     def test_ccld_mode(self):
         self.check_cc('dump-mode', [], "ccld")
         self.check_cc('dump-mode', ['foo.c', '-o', 'foo'], "ccld")
-        self.check_cc('dump-mode', ['foo.c', '-o', 'foo', '-Wl,-rpath=foo'], "ccld")
+        self.check_cc('dump-mode', ['foo.c', '-o', 'foo', '-Wl,-rpath,foo'], "ccld")
-        self.check_cc('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath=foo'], "ccld")
+        self.check_cc('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'], "ccld")
 
 
     def test_ld_mode(self):
         self.check_ld('dump-mode', [], "ld")
-        self.check_ld('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath=foo'], "ld")
+        self.check_ld('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'], "ld")
 
 
     def test_includes(self):

lib/spack/spack/test/concretize.py

@@ -22,8 +22,6 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import unittest
-
 import spack
 from spack.spec import Spec, CompilerSpec
 from spack.test.mock_packages_test import *

lib/spack/spack/test/config.py

@@ -22,13 +22,13 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import unittest
-import shutil
 import os
+import shutil
 from tempfile import mkdtemp
-from ordereddict_backport import OrderedDict
+
 import spack
 import spack.config
+from ordereddict_backport import OrderedDict
 from spack.test.mock_packages_test import *
 
 # Some sample compiler config data

lib/spack/spack/test/configure_guess.py

@@ -23,20 +23,15 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-import unittest
 import shutil
 import tempfile
+import unittest
 
 from llnl.util.filesystem import *
-
 from spack.cmd.create import ConfigureGuesser
 from spack.stage import Stage
-
-from spack.fetch_strategy import URLFetchStrategy
-from spack.directory_layout import YamlDirectoryLayout
-from spack.util.executable import which
 from spack.test.mock_packages_test import *
-from spack.test.mock_repo import MockArchive
+from spack.util.executable import which
 
 
 class InstallTest(unittest.TestCase):
@@ -52,8 +47,6 @@ def setUp(self):
 
     def tearDown(self):
         shutil.rmtree(self.tmpdir, ignore_errors=True)
-        if self.stage:
-            self.stage.destroy()
         os.chdir(self.orig_dir)
 
 
@@ -64,11 +57,11 @@ def check_archive(self, filename, system):
 
         url = 'file://' + join_path(os.getcwd(), 'archive.tar.gz')
         print url
-        self.stage = Stage(url)
+        with Stage(url) as stage:
-        self.stage.fetch()
+            stage.fetch()
 
             guesser = ConfigureGuesser()
-        guesser(self.stage)
+            guesser(stage)
             self.assertEqual(system, guesser.build_system)
 
 

lib/spack/spack/test/database.py

@@ -26,19 +26,18 @@
 These tests check the database is functioning properly,
 both in memory and in its file
 """
-import tempfile
-import shutil
 import multiprocessing
-
+import shutil
-from llnl.util.lock import *
+import tempfile
-from llnl.util.filesystem import join_path
 
 import spack
+from llnl.util.filesystem import join_path
+from llnl.util.lock import *
+from llnl.util.tty.colify import colify
 from spack.database import Database
 from spack.directory_layout import YamlDirectoryLayout
 from spack.test.mock_packages_test import *
 
-from llnl.util.tty.colify import colify
 
 def _print_ref_counts():
     """Print out all ref counts for the graph used here, for debugging"""

lib/spack/spack/test/directory_layout.py

@@ -25,20 +25,17 @@
 """\
 This test verifies that the Spack directory layout works properly.
 """
-import unittest
-import tempfile
-import shutil
 import os
-
+import shutil
-from llnl.util.filesystem import *
+import tempfile
 
 import spack
-from spack.spec import Spec
+from llnl.util.filesystem import *
-from spack.repository import RepoPath
 from spack.directory_layout import YamlDirectoryLayout
+from spack.repository import RepoPath
+from spack.spec import Spec
 from spack.test.mock_packages_test import *
 
-
 # number of packages to test (to reduce test time)
 max_packages = 10
 

lib/spack/spack/test/git_fetch.py

@@ -23,19 +23,12 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-import unittest
-import shutil
-import tempfile
-
-from llnl.util.filesystem import *
 
 import spack
-from spack.version import ver
+from llnl.util.filesystem import *
-from spack.stage import Stage
-from spack.util.executable import which
-
 from spack.test.mock_packages_test import *
 from spack.test.mock_repo import MockGitRepo
+from spack.version import ver
 
 
 class GitFetchTest(MockPackagesTest):
@@ -52,19 +45,15 @@ def setUp(self):
         spec.concretize()
         self.pkg = spack.repo.get(spec, new=True)
 
-
     def tearDown(self):
         """Destroy the stage space used by this test."""
         super(GitFetchTest, self).tearDown()
         self.repo.destroy()
-        self.pkg.do_clean()
-
 
     def assert_rev(self, rev):
         """Check that the current git revision is equal to the supplied rev."""
         self.assertEqual(self.repo.rev_hash('HEAD'), self.repo.rev_hash(rev))
 
-
     def try_fetch(self, rev, test_file, args):
         """Tries to:
            1. Fetch the repo using a fetch strategy constructed with
@@ -76,6 +65,7 @@ def try_fetch(self, rev, test_file, args):
         """
         self.pkg.versions[ver('git')] = args
 
+        with self.pkg.stage:
             self.pkg.do_stage()
             self.assert_rev(rev)
 

lib/spack/spack/test/hg_fetch.py

@@ -23,16 +23,12 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-import unittest
-
-from llnl.util.filesystem import *
-
 import spack
+
 from spack.version import ver
-from spack.stage import Stage
-from spack.util.executable import which
-from spack.test.mock_packages_test import *
 from spack.test.mock_repo import MockHgRepo
+from llnl.util.filesystem import *
+from spack.test.mock_packages_test import *
 
 
 class HgFetchTest(MockPackagesTest):
@@ -49,13 +45,10 @@ def setUp(self):
         spec.concretize()
         self.pkg = spack.repo.get(spec, new=True)
 
-
     def tearDown(self):
         """Destroy the stage space used by this test."""
         super(HgFetchTest, self).tearDown()
         self.repo.destroy()
-        self.pkg.do_clean()
-
 
     def try_fetch(self, rev, test_file, args):
         """Tries to:
@@ -68,6 +61,7 @@ def try_fetch(self, rev, test_file, args):
         """
         self.pkg.versions[ver('hg')] = args
 
+        with self.pkg.stage:
             self.pkg.do_stage()
             self.assertEqual(self.repo.get_rev(), rev)
 

lib/spack/spack/test/install.py

@@ -22,18 +22,13 @@
 # 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 unittest
 import shutil
 import tempfile
 
-from llnl.util.filesystem import *
-
 import spack
-from spack.stage import Stage
+from llnl.util.filesystem import *
-from spack.fetch_strategy import URLFetchStrategy, FetchStrategyComposite
 from spack.directory_layout import YamlDirectoryLayout
-from spack.util.executable import which
+from spack.fetch_strategy import URLFetchStrategy, FetchStrategyComposite
 from spack.test.mock_packages_test import *
 from spack.test.mock_repo import MockArchive
 

lib/spack/spack/test/link_tree.py

@@ -24,8 +24,6 @@
 ##############################################################################
 import os
 import unittest
-import shutil
-import tempfile
 
 from llnl.util.filesystem import *
 from llnl.util.link_tree import LinkTree
@@ -38,6 +36,7 @@ class LinkTreeTest(unittest.TestCase):
 
     def setUp(self):
         self.stage = Stage('link-tree-test')
+        self.stage.create()
 
         with working_dir(self.stage.path):
             touchp('source/1')
@@ -51,9 +50,7 @@ def setUp(self):
         source_path = os.path.join(self.stage.path, 'source')
         self.link_tree = LinkTree(source_path)
 
-
     def tearDown(self):
-        if self.stage:
         self.stage.destroy()
 
 

lib/spack/spack/test/lock.py

@@ -25,15 +25,13 @@
 """
 These tests ensure that our lock works correctly.
 """
-import unittest
-import os
-import tempfile
 import shutil
+import tempfile
+import unittest
 from multiprocessing import Process
 
-from llnl.util.lock import *
 from llnl.util.filesystem import join_path, touch
-
+from llnl.util.lock import *
 from spack.util.multiproc import Barrier
 
 # This is the longest a failed test will take, as the barriers will

lib/spack/spack/test/make_executable.py

@@ -28,13 +28,13 @@
 This just tests whether the right args are getting passed to make.
 """
 import os
-import unittest
-import tempfile
 import shutil
+import tempfile
+import unittest
 
 from llnl.util.filesystem import *
-from spack.util.environment import path_put_first
 from spack.build_environment import MakeExecutable
+from spack.util.environment import path_put_first
 
 
 class MakeExecutableTest(unittest.TestCase):

lib/spack/spack/test/mirror.py

@@ -23,11 +23,10 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-from filecmp import dircmp
-
 import spack
 import spack.mirror
-from spack.util.compression import decompressor_for
+
+from filecmp import dircmp
 from spack.test.mock_packages_test import *
 from spack.test.mock_repo import *
 
@@ -74,14 +73,14 @@ def set_up_package(self, name, MockRepoClass, url_attr):
 
 
     def check_mirror(self):
-        stage = Stage('spack-mirror-test')
+        with Stage('spack-mirror-test') as stage:
             mirror_root = join_path(stage.path, 'test-mirror')
 
             # register mirror with spack config
             mirrors = { 'spack-mirror-test' : 'file://' + mirror_root }
             spack.config.update_config('mirrors', mirrors)
 
-        try:
+
             os.chdir(stage.path)
             spack.mirror.create(
                 mirror_root, self.repos, no_checksum=True)
@@ -102,33 +101,23 @@ def check_mirror(self):
                     spec = Spec(name).concretized()
                     pkg = spec.package
 
-                pkg._stage = None
                     saved_checksum_setting = spack.do_checksum
-                try:
+                    with pkg.stage:
                         # Stage the archive from the mirror and cd to it.
                         spack.do_checksum = False
                         pkg.do_stage(mirror_only=True)
-
                         # Compare the original repo with the expanded archive
                         original_path = mock_repo.path
                         if 'svn' in name:
                             # have to check out the svn repo to compare.
                             original_path = join_path(mock_repo.path, 'checked_out')
                             svn('checkout', mock_repo.url, original_path)
-
                         dcmp = dircmp(original_path, pkg.stage.source_path)
-
                         # make sure there are no new files in the expanded tarball
                         self.assertFalse(dcmp.right_only)
-
                         # and that all original files are present.
                         self.assertTrue(all(l in exclude for l in dcmp.left_only))
-
-                finally:
                         spack.do_checksum = saved_checksum_setting
-                    pkg.do_clean()
-        finally:
-            stage.destroy()
 
 
     def test_git_mirror(self):

lib/spack/spack/test/mock_packages_test.py

@@ -22,17 +22,15 @@
 # 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
 import shutil
-import unittest
 import tempfile
-from ordereddict_backport import OrderedDict
+import unittest
-
-from llnl.util.filesystem import mkdirp
 
 import spack
 import spack.config
+from llnl.util.filesystem import mkdirp
+from ordereddict_backport import OrderedDict
 from spack.repository import RepoPath
 from spack.spec import Spec
 

lib/spack/spack/test/mock_repo.py

@@ -26,13 +26,9 @@
 import shutil
 
 from llnl.util.filesystem import *
-
-import spack
-from spack.version import ver
 from spack.stage import Stage
 from spack.util.executable import which
 
-
 #
 # VCS Systems used by mock repo code.
 #

lib/spack/spack/test/multimethod.py

@@ -25,14 +25,11 @@
 """
 Test for multi_method dispatch.
 """
-import unittest
 
 import spack
 from spack.multimethod import *
-from spack.version import *
-from spack.spec import Spec
-from spack.multimethod import when
 from spack.test.mock_packages_test import *
+from spack.version import *
 
 
 class MultiMethodTest(MockPackagesTest):

lib/spack/spack/test/namespace_trie.py

@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/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
@@ -23,6 +23,7 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import unittest
+
 from spack.util.naming import NamespaceTrie
 
 

lib/spack/spack/test/optional_deps.py

@@ -22,10 +22,8 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import unittest
 
-import spack
+from spack.spec import Spec
-from spack.spec import Spec, CompilerSpec
 from spack.test.mock_packages_test import *
 
 class ConcretizeTest(MockPackagesTest):

lib/spack/spack/test/packages.py

@@ -22,14 +22,12 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import unittest
-
-from llnl.util.filesystem import join_path
 
 import spack
+from llnl.util.filesystem import join_path
 from spack.repository import Repo
-from spack.util.naming import mod_to_class
 from spack.test.mock_packages_test import *
+from spack.util.naming import mod_to_class
 
 
 class PackagesTest(MockPackagesTest):

lib/spack/spack/test/python_version.py

@@ -28,12 +28,11 @@
 Spack was originally 2.7, but enough systems in 2014 are still using
 2.6 on their frontend nodes that we need 2.6 to get adopted.
 """
-import unittest
 import os
 import re
+import unittest
 
 import llnl.util.tty as tty
-
 import pyqver2
 import spack
 

lib/spack/spack/test/spec_dag.py

@@ -31,8 +31,6 @@
 import spack
 import spack.package
 
-from llnl.util.lang import list_modules
-
 from spack.spec import Spec
 from spack.test.mock_packages_test import *
 

lib/spack/spack/test/spec_semantics.py

@@ -22,7 +22,6 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import unittest
 from spack.spec import *
 from spack.test.mock_packages_test import *
 

lib/spack/spack/test/spec_syntax.py

@@ -23,9 +23,10 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import unittest
+
 import spack.spec
-from spack.spec import *
 from spack.parse import Token
+from spack.spec import *
 
 # Sample output for a complex lexing.
 complex_lex = [Token(ID, 'mvapich_foo'),

lib/spack/spack/test/stage.py

@@ -25,15 +25,13 @@
 """\
 Test that the Stage class works correctly.
 """
-import unittest
-import shutil
 import os
-import getpass
+import shutil
+import unittest
 from contextlib import *
 
-from llnl.util.filesystem import *
-
 import spack
+from llnl.util.filesystem import *
 from spack.stage import Stage
 from spack.util.executable import which
 
@@ -192,96 +190,73 @@ def check_destroy(self, stage, stage_name):
 
     def test_setup_and_destroy_name_with_tmp(self):
         with use_tmp(True):
-            stage = Stage(archive_url, name=stage_name)
+            with Stage(archive_url, name=stage_name) as stage:
                 self.check_setup(stage, stage_name)
-
-            stage.destroy()
             self.check_destroy(stage, stage_name)
 
 
     def test_setup_and_destroy_name_without_tmp(self):
         with use_tmp(False):
-            stage = Stage(archive_url, name=stage_name)
+            with Stage(archive_url, name=stage_name) as stage:
                 self.check_setup(stage, stage_name)
-
-            stage.destroy()
             self.check_destroy(stage, stage_name)
 
 
     def test_setup_and_destroy_no_name_with_tmp(self):
         with use_tmp(True):
-            stage = Stage(archive_url)
+            with Stage(archive_url) as stage:
                 self.check_setup(stage, None)
-
-            stage.destroy()
             self.check_destroy(stage, None)
 
 
     def test_setup_and_destroy_no_name_without_tmp(self):
         with use_tmp(False):
-            stage = Stage(archive_url)
+            with Stage(archive_url) as stage:
                 self.check_setup(stage, None)
-
-            stage.destroy()
             self.check_destroy(stage, None)
 
 
     def test_chdir(self):
-        stage = Stage(archive_url, name=stage_name)
+        with Stage(archive_url, name=stage_name) as stage:
-
             stage.chdir()
             self.check_setup(stage, stage_name)
             self.check_chdir(stage, stage_name)
-
-        stage.destroy()
         self.check_destroy(stage, stage_name)
 
 
     def test_fetch(self):
-        stage = Stage(archive_url, name=stage_name)
+        with Stage(archive_url, name=stage_name) as stage:
-
             stage.fetch()
             self.check_setup(stage, stage_name)
             self.check_chdir(stage, stage_name)
             self.check_fetch(stage, stage_name)
-
-        stage.destroy()
         self.check_destroy(stage, stage_name)
 
 
     def test_expand_archive(self):
-        stage = Stage(archive_url, name=stage_name)
+        with Stage(archive_url, name=stage_name) as stage:
-
             stage.fetch()
             self.check_setup(stage, stage_name)
             self.check_fetch(stage, stage_name)
-
             stage.expand_archive()
             self.check_expand_archive(stage, stage_name)
-
-        stage.destroy()
         self.check_destroy(stage, stage_name)
 
 
     def test_expand_archive(self):
-        stage = Stage(archive_url, name=stage_name)
+        with Stage(archive_url, name=stage_name) as stage:
-
             stage.fetch()
             self.check_setup(stage, stage_name)
             self.check_fetch(stage, stage_name)
-
             stage.expand_archive()
             stage.chdir_to_source()
             self.check_expand_archive(stage, stage_name)
             self.check_chdir_to_source(stage, stage_name)
-
-        stage.destroy()
         self.check_destroy(stage, stage_name)
 
 
     def test_restage(self):
-        stage = Stage(archive_url, name=stage_name)
+        with Stage(archive_url, name=stage_name) as stage:
-
             stage.fetch()
             stage.expand_archive()
             stage.chdir_to_source()
@@ -298,10 +273,7 @@ def test_restage(self):
             stage.restage()
             self.check_chdir(stage, stage_name)
             self.check_fetch(stage, stage_name)
-
             stage.chdir_to_source()
             self.check_chdir_to_source(stage, stage_name)
             self.assertFalse('foobar' in os.listdir(stage.source_path))
-
-        stage.destroy()
         self.check_destroy(stage, stage_name)

lib/spack/spack/test/svn_fetch.py

@@ -24,18 +24,12 @@
 ##############################################################################
 import os
 import re
-import unittest
-import shutil
-import tempfile
-
-from llnl.util.filesystem import *
-
 import spack
-from spack.version import ver
+
-from spack.stage import Stage
-from spack.util.executable import which
-from spack.test.mock_packages_test import *
 from spack.test.mock_repo import svn, MockSvnRepo
+from spack.version import ver
+from spack.test.mock_packages_test import *
+from llnl.util.filesystem import *
 
 
 class SvnFetchTest(MockPackagesTest):
@@ -51,13 +45,10 @@ def setUp(self):
         spec.concretize()
         self.pkg = spack.repo.get(spec, new=True)
 
-
     def tearDown(self):
         """Destroy the stage space used by this test."""
         super(SvnFetchTest, self).tearDown()
         self.repo.destroy()
-        self.pkg.do_clean()
-
 
     def assert_rev(self, rev):
         """Check that the current revision is equal to the supplied rev."""
@@ -70,7 +61,6 @@ def get_rev():
                     return match.group(1)
         self.assertEqual(get_rev(), rev)
 
-
     def try_fetch(self, rev, test_file, args):
         """Tries to:
            1. Fetch the repo using a fetch strategy constructed with
@@ -82,6 +72,7 @@ def try_fetch(self, rev, test_file, args):
         """
         self.pkg.versions[ver('svn')] = args
 
+        with self.pkg.stage:
             self.pkg.do_stage()
             self.assert_rev(rev)
 

lib/spack/spack/test/tally_plugin.py

@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://scalability-llnl.github.io/spack
+# For details, see https://scalability-software.llnl.gov/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
@@ -22,10 +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
 ##############################################################################
-from nose.plugins import Plugin
-
 import os
 
+from nose.plugins import Plugin
+
 class Tally(Plugin):
     name = 'tally'
 

lib/spack/spack/test/unit_install.py

@@ -22,10 +22,11 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import unittest
 import itertools
+import unittest
 
 import spack
+
 test_install = __import__("spack.cmd.test-install",
     fromlist=["BuildId", "create_test_output", "TestResult"])
 

lib/spack/spack/test/url_extrapolate.py

@@ -25,10 +25,7 @@
 """\
 Tests ability of spack to extrapolate URL versions from existing versions.
 """
-import spack
 import spack.url as url
-from spack.spec import Spec
-from spack.version import ver
 from spack.test.mock_packages_test import *
 
 

lib/spack/spack/test/url_parse.py

@@ -27,8 +27,8 @@
 detection in Homebrew.
 """
 import unittest
+
 import spack.url as url
-from pprint import pprint
 
 
 class UrlParseTest(unittest.TestCase):

lib/spack/spack/test/url_substitution.py

@@ -27,7 +27,6 @@
 """
 import unittest
 
-import spack
 import spack.url as url
 
 

lib/spack/spack/test/versions.py

@@ -28,6 +28,7 @@
 where it makes sense.
 """
 import unittest
+
 from spack.version import *
 
 

lib/spack/spack/test/yaml.py

@@ -26,6 +26,7 @@
 Test Spack's custom YAML format.
 """
 import unittest
+
 import spack.util.spack_yaml as syaml
 
 test_file = """\

lib/spack/spack/url.py

@@ -225,7 +225,7 @@ def parse_version_offset(path):
         (r'_((\d+\.)+\d+[a-z]?)[.]orig$', stem),
 
         # e.g. http://www.openssl.org/source/openssl-0.9.8s.tar.gz
-        (r'-([^-]+(-alpha|-beta)?)', stem),
+        (r'-v?([^-]+(-alpha|-beta)?)', stem),
 
         # e.g. astyle_1.23_macosx.tar.gz
         (r'_([^_]+(_alpha|_beta)?)', stem),

lib/spack/spack/util/environment.py

@@ -63,3 +63,10 @@ def pop_keys(dictionary, *keys):
     for key in keys:
         if key in dictionary:
             dictionary.pop(key)
+
+
+def dump_environment(path):
+    """Dump the current environment out to a file."""
+    with open(path, 'w') as env_file:
+        for key,val in sorted(os.environ.items()):
+            env_file.write("%s=%s\n" % (key, val))

lib/spack/spack/util/web.py

@@ -86,12 +86,12 @@ def _spider(args):
 
         if not "Content-type" in resp.headers:
             tty.debug("ignoring page " + url)
-            return pages
+            return pages, links
 
         if not resp.headers["Content-type"].startswith('text/html'):
             tty.debug("ignoring page " + url + " with content type " +
                       resp.headers["Content-type"])
-            return pages
+            return pages, links
 
         # Do the real GET request when we know it's just HTML.
         req.get_method = lambda: "GET"

var/spack/repos/builtin/packages/blitz/package.py

@@ -0,0 +1,15 @@
+from spack import *
+
+class Blitz(Package):
+    """N-dimensional arrays for C++"""
+    homepage = "http://github.com/blitzpp/blitz"
+    url      = "https://github.com/blitzpp/blitz/tarball/1.0.0"
+
+    version('1.0.0', '9f040b9827fe22228a892603671a77af')
+
+    # No dependencies
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+        make()
+        make("install")

var/spack/repos/builtin/packages/cgal/package.py

@@ -46,6 +46,7 @@ class Cgal(Package):
     depends_on('mpfr')
     depends_on('gmp')
     depends_on('zlib')
+    depends_on('cmake')
 
     # FIXME : Qt5 dependency missing (needs Qt5 and OpenGL)
     # FIXME : Optional third party libraries missing

var/spack/repos/builtin/packages/expat/package.py

@@ -7,6 +7,7 @@ class Expat(Package):
 
     version('2.1.0', 'dd7dab7a5fea97d2a6a43f511449b7cd')
 
+    depends_on('cmake')
 
     def install(self, spec, prefix):
 

var/spack/repos/builtin/packages/fftw/package.py

@@ -47,6 +47,8 @@ class Fftw(Package):
 
     depends_on('mpi', when='+mpi')
 
+    # TODO : add support for architecture specific optimizations as soon as targets are supported
+
     def install(self, spec, prefix):
         options = ['--prefix=%s' % prefix,
                    '--enable-shared',

var/spack/repos/builtin/packages/gdb/package.py

@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/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

var/spack/repos/builtin/packages/gromacs/package.py

@@ -0,0 +1,56 @@
+from spack import *
+
+
+class Gromacs(Package):
+    """
+    GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for
+    simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry
+    department of University of Groningen, and is now maintained by contributors in universities and research centers
+    across the world.
+
+    GROMACS is one of the fastest and most popular software packages available and can run on CPUs as well as GPUs.
+    It is free, open source released under the GNU General Public License. Starting from version 4.6, GROMACS is
+    released under the GNU Lesser General Public License.
+    """
+
+    homepage = 'http://www.gromacs.org'
+    url = 'ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.1.2.tar.gz'
+
+    version('5.1.2', '614d0be372f1a6f1f36382b7a6fcab98')
+
+    variant('mpi', default=True, description='Activate MPI support')
+    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('debug', default=False, description='Enables debug mode')
+    variant('double', default=False, description='Produces a double precision version of the executables')
+
+    depends_on('mpi', when='+mpi')
+
+    depends_on('fftw')
+
+    # TODO : add GPU support
+
+    def install(self, spec, prefix):
+
+        options = []
+
+        if '+mpi' in spec:
+            options.append('-DGMX_MPI:BOOL=ON')
+
+        if '+double' in spec:
+            options.append('-DGMX_DOUBLE:BOOL=ON')
+
+        if '~shared' in spec:
+            options.append('-DBUILD_SHARED_LIBS:BOOL=OFF')
+
+        if '+debug' in spec:
+            options.append('-DCMAKE_BUILD_TYPE:STRING=Debug')
+        else:
+            options.append('-DCMAKE_BUILD_TYPE:STRING=Release')
+
+        options.extend(std_cmake_args)
+
+        with working_dir('spack-build', create=True):
+
+            cmake('..', *options)
+            make()
+            make('install')

var/spack/repos/builtin/packages/jdk/package.py

@@ -28,7 +28,7 @@ class Jdk(Package):
         '-H', # specify required License Agreement cookie
         'Cookie: oraclelicense=accept-securebackup-cookie']
 
-    def do_fetch(self):
+    def do_fetch(self, mirror_only=False):
         # Add our custom curl commandline options
         tty.msg(
             "[Jdk] Adding required commandline options to curl " +
@@ -39,7 +39,7 @@ def do_fetch(self):
             spack.curl.add_default_arg(option)
 
         # Now perform the actual fetch
-        super(Jdk, self).do_fetch()
+        super(Jdk, self).do_fetch(mirror_only)
 
 
     def install(self, spec, prefix):

var/spack/repos/builtin/packages/libevent/package.py

@@ -22,9 +22,16 @@ class Libevent(Package):
     version('2.0.13', 'af786b4b3f790c9d3279792edf7867fc')
     version('2.0.12', '42986228baf95e325778ed328a93e070')
 
+    variant('openssl', default=True, description="Build with encryption enabled at the libevent level.")
+    depends_on('openssl', when='+openssl')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix)
+        configure_args = []
+        if '+openssl' in spec:
+            configure_args.append('--enable-openssl')
+        else:
+            configure_args.append('--enable-openssl')
 
+        configure("--prefix=%s" % prefix, *configure_args)
         make()
         make("install")

var/spack/repos/builtin/packages/libsigsegv/package.py

@@ -0,0 +1,15 @@
+from spack import *
+
+class Libsigsegv(Package):
+    """GNU libsigsegv is a library for handling page faults in user mode."""
+    homepage = "https://www.gnu.org/software/libsigsegv/"
+    url      = "ftp://ftp.gnu.org/gnu/libsigsegv/libsigsegv-2.10.tar.gz"
+
+    version('2.10', '7f96fb1f65b3b8cbc1582fb7be774f0f')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix,
+                  '--enable-shared')
+
+        make()
+        make("install")

var/spack/repos/builtin/packages/llvm/package.py

@@ -1,5 +1,5 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
@@ -34,7 +34,7 @@ class Llvm(Package):
        it is the full name of the project.
     """
     homepage = 'http://llvm.org/'
-    url = 'http://llvm.org/releases/3.7.0/llvm-3.7.0.src.tar.xz'
+    url = 'http://llvm.org/releases/3.7.1/llvm-3.7.1.src.tar.xz'
 
     version('3.0', 'a8e5f5f1c1adebae7b4a654c376a6005', url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz') # currently required by mesa package
 
@@ -117,6 +117,36 @@ class Llvm(Package):
                     },
                 }
     releases = [
+                  {
+                    'version' : 'trunk',
+                    'repo' : 'http://llvm.org/svn/llvm-project/llvm/trunk',
+                    'resources' : {
+                        'compiler-rt' : 'http://llvm.org/svn/llvm-project/compiler-rt/trunk',
+                        'openmp' : 'http://llvm.org/svn/llvm-project/openmp/trunk',
+                        'polly' : 'http://llvm.org/svn/llvm-project/polly/trunk',
+                        'libcxx' : 'http://llvm.org/svn/llvm-project/libcxx/trunk',
+                        'libcxxabi' : 'http://llvm.org/svn/llvm-project/libcxxabi/trunk',
+                        'clang' : 'http://llvm.org/svn/llvm-project/cfe/trunk',
+                        'clang-tools-extra' : 'http://llvm.org/svn/llvm-project/clang-tools-extra/trunk',
+                        'lldb' : 'http://llvm.org/svn/llvm-project/lldb/trunk',
+                        'llvm-libunwind' : 'http://llvm.org/svn/llvm-project/libunwind/trunk',
+                        }
+                  },
+                  {
+                    'version' : '3.7.1',
+                    'md5':'bf8b3a2c79e61212c5409041dfdbd319',
+                    'resources' : {
+                        'compiler-rt' : '1c6975daf30bb3b0473b53c3a1a6ff01',
+                        'openmp' : 'b4ad08cda4e5c22e42b66062b140438e',
+                        'polly' : '3a2a7367002740881637f4d47bca4dc3',
+                        'libcxx' : 'f9c43fa552a10e14ff53b94d04bea140',
+                        'libcxxabi' : '52d925afac9f97e9dcac90745255c169',
+                        'clang' : '0acd026b5529164197563d135a8fd83e',
+                        'clang-tools-extra' : '5d49ff745037f061a7c86aeb6a24c3d2',
+                        'lldb' : 'a106d8a0d21fc84d76953822fbaf3398',
+                        'llvm-libunwind' : '814bd52c9247c5d04629658fbcb3ab8c',
+                        }
+                  },
                   {
                     'version' : '3.7.0',
                     'md5':'b98b9495e5655a672d6cb83e1a180f8e',
@@ -161,6 +191,16 @@ class Llvm(Package):
                ]
 
     for release in releases:
+        if release['version'] == 'trunk' :
+            version(release['version'], svn=release['repo'])
+
+            for name, repo in release['resources'].items():
+                resource(name=name,
+                         svn=repo,
+                         destination=resources[name]['destination'],
+                         when='@%(version)s' % release,
+                         placement=resources[name].get('placement', None))
+        else:
             version(release['version'], release['md5'], url=llvm_url % release)
 
             for name, md5 in release['resources'].items():
@@ -171,25 +211,6 @@ class Llvm(Package):
                          when='@%(version)s' % release,
                          placement=resources[name].get('placement', None))
 
-    # SVN - current develop
-    version('develop', svn='http://llvm.org/svn/llvm-project/llvm/trunk')
-    resource(name='clang', svn='http://llvm.org/svn/llvm-project/cfe/trunk',
-             destination='tools', when='@develop', placement='clang')
-    resource(name='compiler-rt', svn='http://llvm.org/svn/llvm-project/compiler-rt/trunk',
-             destination='projects', when='@develop', placement='compiler-rt')
-    resource(name='openmp', svn='http://llvm.org/svn/llvm-project/openmp/trunk',
-             destination='projects', when='@develop', placement='openmp')
-    resource(name='libcxx', svn='http://llvm.org/svn/llvm-project/libcxx/trunk',
-             destination='projects', when='@develop', placement='libcxx')
-    resource(name='libcxxabi', svn='http://llvm.org/svn/llvm-project/libcxxabi/trunk',
-             destination='projects', when='@develop', placement='libcxxabi')
-    resource(name='polly', svn='http://llvm.org/svn/llvm-project/polly/trunk',
-             destination='tools', when='@develop', placement='polly')
-    resource(name='lldb', svn='http://llvm.org/svn/llvm-project/lldb/trunk',
-             destination='tools', when='@develop', placement='lldb')
-
-
-
     def install(self, spec, prefix):
         env['CXXFLAGS'] = self.compiler.cxx11_flag
         cmake_args = [ arg for arg in std_cmake_args if 'BUILD_TYPE' not in arg ]

var/spack/repos/builtin/packages/m4/package.py

@@ -7,7 +7,17 @@ class M4(Package):
 
     version('1.4.17', 'a5e9954b1dae036762f7b13673a2cf76')
 
+    variant('sigsegv', default=True, description="Build the libsigsegv dependency")
+
+    depends_on('libsigsegv', when='+sigsegv')
+
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix)
+        configure_args = []
+        if 'libsigsegv' in spec:
+            configure_args.append('--with-libsigsegv-prefix=%s' % spec['libsigsegv'].prefix)
+        else:
+            configure_args.append('--without-libsigsegv-prefix')
+
+        configure("--prefix=%s" % prefix, *configure_args)
         make()
         make("install")

var/spack/repos/builtin/packages/mpc/package.py

@@ -37,6 +37,12 @@ class Mpc(Package):
     depends_on("gmp")
     depends_on("mpfr")
 
+    def url_for_version(self, version):
+        if version < Version("1.0.1"):
+            return "http://www.multiprecision.org/mpc/download/mpc-%s.tar.gz" % version
+        else:
+            return "ftp://ftp.gnu.org/gnu/mpc/mpc-%s.tar.gz" % version
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()

var/spack/repos/builtin/packages/netcdf-cxx4/package.py

@@ -0,0 +1,15 @@
+from spack import *
+
+class NetcdfCxx4(Package):
+    """C++ interface for NetCDF4"""
+    homepage = "http://www.unidata.ucar.edu/software/netcdf"
+    url      = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx4-4.2.tar.gz"
+
+    version('4.2', 'd019853802092cf686254aaba165fc81')
+
+    depends_on('netcdf')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+        make()
+        make("install")

var/spack/repos/builtin/packages/netcdf-fortran/package.py

@@ -0,0 +1,16 @@
+from spack import *
+
+class NetcdfFortran(Package):
+    """Fortran interface for NetCDF4"""
+
+    homepage = "http://www.unidata.ucar.edu/software/netcdf"
+    url      = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.4.3.tar.gz"
+
+    version('4.4.3', 'bfd4ae23a34635b273d3eb0d91cbde9e')
+
+    depends_on('netcdf')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+        make()
+        make("install")

var/spack/repos/builtin/packages/netcdf/package.py

@@ -6,14 +6,13 @@ class Netcdf(Package):
     data formats that support the creation, access, and sharing of array-oriented
     scientific data."""
 
-    homepage = "http://www.unidata.ucar.edu/software/netcdf/"
+    homepage = "http://www.unidata.ucar.edu/software/netcdf"
     url      = "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.tar.gz"
 
     version('4.4.0', 'cffda0cbd97fdb3a06e9274f7aef438e')
     version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae')
 
     variant('mpi', default=True, description='Enables MPI parallelism')
-    variant('fortran', default=False, description="Download and install NetCDF-Fortran")
     variant('hdf4',    default=False, description="Enable HDF4 support")
 
     # Dependencies:
@@ -66,11 +65,7 @@ def install(self, spec, prefix):
 
         # Fortran support
         # In version 4.2+, NetCDF-C and NetCDF-Fortran have split.
-        # They can be installed separately, but this bootstrap procedure
+        # Use the netcdf-fortran package to install Fortran support.
-        # should be able to install both at the same time.
-        # Note: this is a new experimental feature.
-        if '+fortran' in spec:
-            config_args.append("--enable-remote-fortran-bootstrap")
 
         config_args.append('CPPFLAGS=%s' % ' '.join(CPPFLAGS))
         config_args.append('LDFLAGS=%s'  % ' '.join(LDFLAGS))
@@ -79,8 +74,3 @@ def install(self, spec, prefix):
         configure(*config_args)
         make()
         make("install")
-
-        # After installing NetCDF-C, install NetCDF-Fortran
-        if '+fortran' in spec:
-            make("build-netcdf-fortran")
-            make("install-netcdf-fortran")

var/spack/repos/builtin/packages/openssl/package.py

@@ -17,6 +17,7 @@ class Openssl(Package):
     version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a')
     version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5')
     version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d')
+    version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa')
 
     depends_on("zlib")
     parallel = False

var/spack/repos/builtin/packages/pango/package.py

@@ -16,4 +16,4 @@ class Pango(Package):
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()
-        make("install")
+        make("install", parallel=False)

var/spack/repos/builtin/packages/paraview/package.py

@@ -2,9 +2,11 @@
 
 class Paraview(Package):
     homepage = 'http://www.paraview.org'
-    url      = 'http://www.paraview.org/files/v4.4/ParaView-v4.4.0-source.tar.gz'
+    url      = 'http://www.paraview.org/files/v5.0/ParaView-v'
+    _url_str = 'http://www.paraview.org/files/v%s/ParaView-v%s-source.tar.gz'
 
-    version('4.4.0', 'fa1569857dd680ebb4d7ff89c2227378', url='http://www.paraview.org/files/v4.4/ParaView-v4.4.0-source.tar.gz')
+    version('4.4.0', 'fa1569857dd680ebb4d7ff89c2227378')
+    version('5.0.0', '4598f0b421460c8bbc635c9a1c3bdbee')
 
     variant('python', default=False, description='Enable Python support')
 
@@ -25,8 +27,8 @@ class Paraview(Package):
 
     depends_on('bzip2')
     depends_on('freetype')
-    depends_on('hdf5')
     depends_on('hdf5+mpi', when='+mpi')
+    depends_on('hdf5~mpi', when='~mpi')
     depends_on('jpeg')
     depends_on('libpng')
     depends_on('libtiff')
@@ -36,6 +38,11 @@ class Paraview(Package):
     #depends_on('sqlite') # external version not supported
     depends_on('zlib')
     
+    def url_for_version(self, version):
+        """Handle ParaView version-based custom URLs."""
+        return self._url_str % (version.up_to(2), version)
+    
+
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):
             def feature_to_bool(feature, on='ON', off='OFF'):

var/spack/repos/builtin/packages/proj/package.py

@@ -0,0 +1,20 @@
+from spack import *
+
+class Proj(Package):
+    """Cartographic Projections"""
+    homepage = "https://github.com/OSGeo/proj.4/wiki"
+    url      = "http://download.osgeo.org/proj/proj-4.9.2.tar.gz"
+
+    version('4.9.2', '9843131676e31bbd903d60ae7dc76cf9')
+    version('4.9.1', '3cbb2a964fd19a496f5f4265a717d31c')
+    version('4.8.0', 'd815838c92a29179298c126effbb1537')
+    version('4.7.0', '927d34623b52e0209ba2bfcca18fe8cd')
+    version('4.6.1', '7dbaab8431ad50c25669fd3fb28dc493')
+
+    # No dependencies
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")

var/spack/repos/builtin/packages/python/package.py

@@ -55,6 +55,20 @@ def install(self, spec, prefix):
         make()
         make("install")
 
+        # Modify compiler paths in configuration files. This is necessary for
+        # building site packages outside of spack
+        filter_file(r'([/s]=?)([\S=]*)/lib/spack/env(/[^\s/]*)?/(\S*)(\s)',
+                    (r'\4\5'),
+                    join_path(prefix.lib, 'python%d.%d' % self.version[:2], '_sysconfigdata.py'))
+
+        python3_version = ''
+        if spec.satisfies('@3:'):
+            python3_version = '-%d.%dm' % self.version[:2]
+        makefile_filepath = join_path(prefix.lib, 'python%d.%d' % self.version[:2], 'config%s' % python3_version, 'Makefile')
+        filter_file(r'([/s]=?)([\S=]*)/lib/spack/env(/[^\s/]*)?/(\S*)(\s)',
+                    (r'\4\5'),
+                    makefile_filepath)
+
 
     # ========================================================================
     # Set up environment to make install easy for python extensions.

var/spack/repos/builtin/packages/silo/package.py

@@ -1,19 +1,28 @@
 from spack import *
 
 class Silo(Package):
-    """Silo is a library for reading and writing a wide variety of scientific data to binary, disk files."""
+    """Silo is a library for reading and writing a wide variety of scientific
+       data to binary, disk files."""
 
     homepage = "http://wci.llnl.gov/simulation/computer-codes/silo"
     url      = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.8/silo-4.8.tar.gz"
 
-    #version('4.9', 'a83eda4f06761a86726e918fc55e782a')
     version('4.8', 'b1cbc0e7ec435eb656dc4b53a23663c9')
 
-    depends_on("hdf5@:1.8.12")
+    variant('fortran', default=True, description='Enable Fortran support')
+
+    depends_on("hdf5")
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix,
+        config_args = [
-                  "--with-hdf5=%s" %spec['hdf5'].prefix)
+            '--enable-fortran' if '+fortran' in spec else '--disable-fortran',
+        ]
+
+        configure(
+            "--prefix=%s" % prefix,
+            "--with-hdf5=%s,%s" % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib),
+            "--with-zlib=%s,%s" % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib),
+            *config_args)
 
         make()
         make("install")

var/spack/repos/builtin/packages/texinfo/package.py

@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/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

var/spack/repos/builtin/packages/udunits2/package.py

@@ -0,0 +1,16 @@
+from spack import *
+
+class Udunits2(Package):
+    """Automated units conversion"""
+
+    homepage = "http://www.unidata.ucar.edu/software/udunits"
+    url      = "ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.2.20.tar.gz"
+
+    version('2.2.20', '1586b70a49dfe05da5fcc29ef239dce0')
+
+    depends_on('expat')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+        make()
+        make("install")

var/spack/repos/builtin/packages/zfp/package.py

@@ -0,0 +1,26 @@
+from spack import *
+
+class Zfp(Package):
+    """zfp is an open source C library for compressed floating-point arrays that supports
+       very high throughput read and write random acces, target error bounds or bit rates.
+       Although bit-for-bit lossless compression is not always possible, zfp is usually
+       accurate to within machine epsilon in near-lossless mode, and is often orders of
+       magnitude more accurate than other lossy compressors.
+    """
+
+    homepage = "http://computation.llnl.gov/projects/floating-point-compression"
+    url      = "http://computation.llnl.gov/projects/floating-point-compression/download/zfp-0.5.0.tar.gz"
+
+    version('0.5.0', '2ab29a852e65ad85aae38925c5003654')
+
+    def install(self, spec, prefix):
+        make("shared")
+
+        # No install provided
+        mkdirp(prefix.lib)
+        mkdirp(prefix.include)
+        install('lib/libzfp.so', prefix.lib)
+        install('inc/zfp.h', prefix.include)
+        install('inc/types.h', prefix.include)
+        install('inc/bitstream.h', prefix.include)
+        install('inc/system.h', prefix.include)