Merge remote-tracking branch 'upstream/develop' into efischer/160311-StagedPackage

# Conflicts:
#	lib/spack/spack/package.py

lib/spack/docs/mirrors.rst

@@ -38,7 +38,7 @@ contains tarballs for each package, named after each package.
 
 .. note::
 
-   Archives are **not** named exactly they were in the package's fetch
+   Archives are **not** named exactly the way they were in the package's fetch
    URL.  They have the form ``<name>-<version>.<extension>``, where
    ``<name>`` is Spack's name for the package, ``<version>`` is the
    version of the tarball, and ``<extension>`` is whatever format the

lib/spack/docs/packaging_guide.rst

@@ -1559,11 +1559,11 @@ you ask for a particular spec.
 A user may have certain preferences for how packages should
 be concretized on their system.  For example, one user may prefer packages
 built with OpenMPI and the Intel compiler.  Another user may prefer
-packages be built with MVAPICH and GCC.  
+packages be built with MVAPICH and GCC.
 
 Spack can be configured to prefer certain compilers, package
 versions, depends_on, and variants during concretization.
-The preferred configuration can be controlled via the 
+The preferred configuration can be controlled via the
 ``~/.spack/packages.yaml`` file for user configuations, or the
 ``etc/spack/packages.yaml`` site configuration.
 
@@ -1582,32 +1582,32 @@ Here's an example packages.yaml file that sets preferred packages:
         compiler: [gcc@4.4.7, gcc@4.6:, intel, clang, pgi]
         providers:
           mpi: [mvapich, mpich, openmpi]
-          
+
 
 At a high level, this example is specifying how packages should be
-concretized.  The dyninst package should prefer using gcc 4.9 and 
+concretized.  The dyninst package should prefer using gcc 4.9 and
 be built with debug options.  The gperftools package should prefer version
 2.2 over 2.4.  Every package on the system should prefer mvapich for
-its MPI and gcc 4.4.7 (except for Dyninst, which overrides this by preferring gcc 4.9).  
-These options are used to fill in implicit defaults.  Any of them can be overwritten 
+its MPI and gcc 4.4.7 (except for Dyninst, which overrides this by preferring gcc 4.9).
+These options are used to fill in implicit defaults.  Any of them can be overwritten
 on the command line if explicitly requested.
 
-Each packages.yaml file begins with the string ``packages:`` and 
+Each packages.yaml file begins with the string ``packages:`` and
 package names are specified on the next level. The special string ``all``
-applies settings to each package. Underneath each package name is 
-one or more components: ``compiler``, ``variants``, ``version``, 
-or ``providers``.  Each component has an ordered list of spec 
+applies settings to each package. Underneath each package name is
+one or more components: ``compiler``, ``variants``, ``version``,
+or ``providers``.  Each component has an ordered list of spec
 ``constraints``, with earlier entries in the list being preferred over
 later entries.
 
-Sometimes a package installation may have constraints that forbid 
+Sometimes a package installation may have constraints that forbid
 the first concretization rule, in which case Spack will use the first
 legal concretization rule.  Going back to the example, if a user
-requests gperftools 2.3 or later, then Spack will install version 2.4 
+requests gperftools 2.3 or later, then Spack will install version 2.4
 as the 2.4 version of gperftools is preferred over 2.3.
 
-An explicit concretization rule in the preferred section will always 
-take preference over unlisted concretizations.  In the above example, 
+An explicit concretization rule in the preferred section will always
+take preference over unlisted concretizations.  In the above example,
 xlc isn't listed in the compiler list.  Every listed compiler from
 gcc to pgi will thus be preferred over the xlc compiler.
 
@@ -1844,6 +1844,20 @@ dedicated process.
 
 .. _prefix-objects:
 
+
+Failing the build
+----------------------
+
+Sometimes you don't want a package to successfully install unless some
+condition is true.  You can explicitly cause the build to fail from
+``install()`` by raising an ``InstallError``, for example:
+
+.. code-block:: python
+
+   if spec.architecture.startswith('darwin'):
+       raise InstallError('This package does not build on Mac OS X!')
+
+
 Prefix objects
 ----------------------
 
@@ -2160,6 +2174,62 @@ package, this allows us to avoid race conditions in the library's
 build system.
 
 
+.. _sanity-checks:
+
+Sanity checking an intallation
+--------------------------------
+
+By default, Spack assumes that a build has failed if nothing is
+written to the install prefix, and that it has succeeded if anything
+(a file, a directory, etc.)  is written to the install prefix after
+``install()`` completes.
+
+Consider a simple autotools build like this:
+
+.. code-block:: python
+
+   def install(self, spec, prefix):
+       configure("--prefix=" + prefix)
+       make()
+       make("install")
+
+If you are using using standard autotools or CMake, ``configure`` and
+``make`` will not write anything to the install prefix.  Only ``make
+install`` writes the files, and only once the build is already
+complete.  Not all builds are like this.  Many builds of scientific
+software modify the install prefix *before* ``make install``. Builds
+like this can falsely report that they were successfully installed if
+an error occurs before the install is complete but after files have
+been written to the ``prefix``.
+
+
+``sanity_check_is_file`` and ``sanity_check_is_dir``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+You can optionally specify *sanity checks* to deal with this problem.
+Add properties like this to your package:
+
+.. code-block:: python
+
+   class MyPackage(Package):
+       ...
+
+       sanity_check_is_file = ['include/libelf.h']
+       sanity_check_is_dir  = [lib]
+
+       def install(self, spec, prefix):
+           configure("--prefix=" + prefix)
+           make()
+           make("install")
+
+Now, after ``install()`` runs, Spack will check whether
+``$prefix/include/libelf.h`` exists and is a file, and whether
+``$prefix/lib`` exists and is a directory.  If the checks fail, then
+the build will fail and the install prefix will be removed.  If they
+succeed, Spack considers the build succeeful and keeps the prefix in
+place.
+
+
 .. _file-manipulation:
 
 File manipulation functions

lib/spack/llnl/util/lang.py

@@ -235,11 +235,11 @@ def setter(name, value):
     if not has_method(cls, '_cmp_key'):
         raise TypeError("'%s' doesn't define _cmp_key()." % cls.__name__)
 
-    setter('__eq__', lambda s,o: o is not None and s._cmp_key() == o._cmp_key())
+    setter('__eq__', lambda s,o: (s is o) or (o is not None and s._cmp_key() == o._cmp_key()))
     setter('__lt__', lambda s,o: o is not None and s._cmp_key() <  o._cmp_key())
     setter('__le__', lambda s,o: o is not None and s._cmp_key() <= o._cmp_key())
 
-    setter('__ne__', lambda s,o: o is None or s._cmp_key() != o._cmp_key())
+    setter('__ne__', lambda s,o: (s is not o) and (o is None or s._cmp_key() != o._cmp_key()))
     setter('__gt__', lambda s,o: o is None or s._cmp_key() >  o._cmp_key())
     setter('__ge__', lambda s,o: o is None or s._cmp_key() >= o._cmp_key())
 

lib/spack/spack/__init__.py

@@ -188,3 +188,10 @@
 import spack.util.executable
 from spack.util.executable import *
 __all__ += spack.util.executable.__all__
+
+from spack.package import \
+    install_dependency_symlinks, flatten_dependencies, DependencyConflictError, \
+    InstallError, ExternalPackageError
+__all__ += [
+    'install_dependency_symlinks', 'flatten_dependencies', 'DependencyConflictError',
+    'InstallError', 'ExternalPackageError']

lib/spack/spack/build_environment.py

@@ -3,7 +3,7 @@
 build environment.  All of this is set up by package.py just before
 install() is called.
 
-There are two parts to the bulid environment:
+There are two parts to the build environment:
 
 1. Python build environment (i.e. install() method)
 
@@ -13,7 +13,7 @@
    the package's module scope.  Ths allows package writers to call
    them all directly in Package.install() without writing 'self.'
    everywhere.  No, this isn't Pythonic.  Yes, it makes the code more
-   readable and more like the shell script from whcih someone is
+   readable and more like the shell script from which someone is
    likely porting.
 
 2. Build execution environment
@@ -27,17 +27,18 @@
 Skimming this module is a nice way to get acquainted with the types of
 calls you can make from within the install() function.
 """
-import os
-import sys
-import shutil
 import multiprocessing
+import os
 import platform
-from llnl.util.filesystem import *
+import shutil
+import sys
 
 import spack
-import spack.compilers as compilers
-from spack.util.executable import Executable, which
+import llnl.util.tty as tty
+from llnl.util.filesystem import *
+from spack.environment import EnvironmentModifications, validate
 from spack.util.environment import *
+from spack.util.executable import Executable, which
 
 #
 # This can be set by the user to globally disable parallel builds.
@@ -83,85 +84,88 @@ def __call__(self, *args, **kwargs):
         return super(MakeExecutable, self).__call__(*args, **kwargs)
 
 
-def set_compiler_environment_variables(pkg):
-    assert(pkg.spec.concrete)
-    compiler = pkg.compiler
-
+def set_compiler_environment_variables(pkg, env):
+    assert pkg.spec.concrete
     # Set compiler variables used by CMake and autotools
-    assert all(key in pkg.compiler.link_paths
-               for key in ('cc', 'cxx', 'f77', 'fc'))
+    assert all(key in pkg.compiler.link_paths for key in ('cc', 'cxx', 'f77', 'fc'))
 
+    # Populate an object with the list of environment modifications
+    # and return it
+    # TODO : add additional kwargs for better diagnostics, like requestor, ttyout, ttyerr, etc.
     link_dir = spack.build_env_path
-    os.environ['CC']  = join_path(link_dir, pkg.compiler.link_paths['cc'])
-    os.environ['CXX'] = join_path(link_dir, pkg.compiler.link_paths['cxx'])
-    os.environ['F77'] = join_path(link_dir, pkg.compiler.link_paths['f77'])
-    os.environ['FC']  = join_path(link_dir, pkg.compiler.link_paths['fc'])
+    env.set('CC', join_path(link_dir, pkg.compiler.link_paths['cc']))
+    env.set('CXX', join_path(link_dir, pkg.compiler.link_paths['cxx']))
+    env.set('F77', join_path(link_dir, pkg.compiler.link_paths['f77']))
+    env.set('FC', join_path(link_dir, pkg.compiler.link_paths['fc']))
 
     # Set SPACK compiler variables so that our wrapper knows what to call
+    compiler = pkg.compiler
     if compiler.cc:
-        os.environ['SPACK_CC']  = compiler.cc
+        env.set('SPACK_CC', compiler.cc)
     if compiler.cxx:
-        os.environ['SPACK_CXX'] = compiler.cxx
+        env.set('SPACK_CXX', compiler.cxx)
     if compiler.f77:
-        os.environ['SPACK_F77'] = compiler.f77
+        env.set('SPACK_F77', compiler.f77)
     if compiler.fc:
-        os.environ['SPACK_FC']  = compiler.fc
+        env.set('SPACK_FC', compiler.fc)
 
-    os.environ['SPACK_COMPILER_SPEC']  = str(pkg.spec.compiler)
+    env.set('SPACK_COMPILER_SPEC', str(pkg.spec.compiler))
+    return env
 
 
-def set_build_environment_variables(pkg):
-    """This ensures a clean install environment when we build packages.
+def set_build_environment_variables(pkg, env):
+    """
+    This ensures a clean install environment when we build packages
     """
     # Add spack build environment path with compiler wrappers first in
     # the path. We add both spack.env_path, which includes default
     # wrappers (cc, c++, f77, f90), AND a subdirectory containing
     # compiler-specific symlinks.  The latter ensures that builds that
     # are sensitive to the *name* of the compiler see the right name
-    # when we're building wtih the wrappers.
+    # when we're building with the wrappers.
     #
     # Conflicts on case-insensitive systems (like "CC" and "cc") are
     # handled by putting one in the <build_env_path>/case-insensitive
     # directory.  Add that to the path too.
     env_paths = []
-    def add_env_path(path):
-        env_paths.append(path)
-        ci = join_path(path, 'case-insensitive')
-        if os.path.isdir(ci): env_paths.append(ci)
-    add_env_path(spack.build_env_path)
-    add_env_path(join_path(spack.build_env_path, pkg.compiler.name))
+    for item in [spack.build_env_path, join_path(spack.build_env_path, pkg.compiler.name)]:
+        env_paths.append(item)
+        ci = join_path(item, 'case-insensitive')
+        if os.path.isdir(ci):
+            env_paths.append(ci)
 
-    path_put_first("PATH", env_paths)
-    path_set(SPACK_ENV_PATH, env_paths)
+    for item in reversed(env_paths):
+        env.prepend_path('PATH', item)
+    env.set_path(SPACK_ENV_PATH, env_paths)
 
-    # Prefixes of all of the package's dependencies go in
-    # SPACK_DEPENDENCIES
+    # Prefixes of all of the package's dependencies go in SPACK_DEPENDENCIES
     dep_prefixes = [d.prefix for d in pkg.spec.traverse(root=False)]
-    path_set(SPACK_DEPENDENCIES, dep_prefixes)
+    env.set_path(SPACK_DEPENDENCIES, dep_prefixes)
+    env.set_path('CMAKE_PREFIX_PATH', dep_prefixes)  # Add dependencies to CMAKE_PREFIX_PATH
 
     # Install prefix
-    os.environ[SPACK_PREFIX] = pkg.prefix
+    env.set(SPACK_PREFIX, pkg.prefix)
 
     # Install root prefix
-    os.environ[SPACK_INSTALL] = spack.install_path
+    env.set(SPACK_INSTALL, spack.install_path)
 
     # Remove these vars from the environment during build because they
     # can affect how some packages find libraries.  We want to make
     # sure that builds never pull in unintended external dependencies.
-    pop_keys(os.environ, "LD_LIBRARY_PATH", "LD_RUN_PATH", "DYLD_LIBRARY_PATH")
+    env.unset('LD_LIBRARY_PATH')
+    env.unset('LD_RUN_PATH')
+    env.unset('DYLD_LIBRARY_PATH')
 
     # Add bin directories from dependencies to the PATH for the build.
-    bin_dirs = ['%s/bin' % prefix for prefix in dep_prefixes]
-    path_put_first('PATH', [bin for bin in bin_dirs if os.path.isdir(bin)])
+    bin_dirs = reversed(filter(os.path.isdir, ['%s/bin' % prefix for prefix in dep_prefixes]))
+    for item in bin_dirs:
+        env.prepend_path('PATH', item)
 
     # Working directory for the spack command itself, for debug logs.
     if spack.debug:
-        os.environ[SPACK_DEBUG] = "TRUE"
-    os.environ[SPACK_SHORT_SPEC] = pkg.spec.short_spec
-    os.environ[SPACK_DEBUG_LOG_DIR] = spack.spack_working_dir
-
-    # Add dependencies to CMAKE_PREFIX_PATH
-    path_set("CMAKE_PREFIX_PATH", dep_prefixes)
+        env.set(SPACK_DEBUG, 'TRUE')
+    env.set(SPACK_SHORT_SPEC, pkg.spec.short_spec)
+    env.set(SPACK_DEBUG_LOG_DIR, spack.spack_working_dir)
 
     # Add any pkgconfig directories to PKG_CONFIG_PATH
     pkg_config_dirs = []
@@ -170,10 +174,12 @@ def add_env_path(path):
             pcdir = join_path(p, libdir, 'pkgconfig')
             if os.path.isdir(pcdir):
                 pkg_config_dirs.append(pcdir)
-    path_set("PKG_CONFIG_PATH", pkg_config_dirs)
+    env.set_path('PKG_CONFIG_PATH', pkg_config_dirs)
+
+    return env
 
 
-def set_module_variables_for_package(pkg, m):
+def set_module_variables_for_package(pkg, module):
     """Populate the module scope of install() with some useful functions.
        This makes things easier for package writers.
     """
@@ -183,6 +189,8 @@ def set_module_variables_for_package(pkg, m):
         jobs = 1
     elif pkg.make_jobs:
         jobs = pkg.make_jobs
+
+    m = module
     m.make_jobs = jobs
 
     # TODO: make these build deps that can be installed if not found.
@@ -217,7 +225,7 @@ def set_module_variables_for_package(pkg, m):
     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'])
+    m.spack_fc  = join_path(link_dir, pkg.compiler.link_paths['fc'])
 
     # Emulate some shell commands for convenience
     m.pwd          = os.getcwd
@@ -262,24 +270,63 @@ def parent_class_modules(cls):
     return result
 
 
+def setup_module_variables_for_dag(pkg):
+    """Set module-scope variables for all packages in the DAG."""
+    for spec in pkg.spec.traverse(order='post'):
+        # If a user makes their own package repo, e.g.
+        # spack.repos.mystuff.libelf.Libelf, and they inherit from
+        # an existing class like spack.repos.original.libelf.Libelf,
+        # then set the module variables for both classes so the
+        # parent class can still use them if it gets called.
+        spkg = spec.package
+        modules = parent_class_modules(spkg.__class__)
+        for mod in modules:
+            set_module_variables_for_package(spkg, mod)
+        set_module_variables_for_package(spkg, spkg.module)
+
+
 def setup_package(pkg):
     """Execute all environment setup routines."""
-    set_compiler_environment_variables(pkg)
-    set_build_environment_variables(pkg)
+    spack_env = EnvironmentModifications()
+    run_env   = EnvironmentModifications()
 
-    # If a user makes their own package repo, e.g.
-    # spack.repos.mystuff.libelf.Libelf, and they inherit from
-    # an existing class like spack.repos.original.libelf.Libelf,
-    # then set the module variables for both classes so the
-    # parent class can still use them if it gets called.
-    modules = parent_class_modules(pkg.__class__)
-    for mod in modules:
-        set_module_variables_for_package(pkg, mod)
+    # Before proceeding, ensure that specs and packages are consistent
+    #
+    # This is a confusing behavior due to how packages are
+    # constructed.  `setup_dependent_package` may set attributes on
+    # specs in the DAG for use by other packages' install
+    # method. However, spec.package will look up a package via
+    # spack.repo, which defensively copies specs into packages.  This
+    # code ensures that all packages in the DAG have pieces of the
+    # same spec object at build time.
+    #
+    # This is safe for the build process, b/c the build process is a
+    # throwaway environment, but it is kind of dirty.
+    #
+    # TODO: Think about how to avoid this fix and do something cleaner.
+    for s in pkg.spec.traverse(): s.package.spec = s
 
-    # Allow dependencies to set up environment as well.
-    for dep_spec in pkg.spec.traverse(root=False):
-        dep_spec.package.setup_dependent_environment(
-            pkg.module, dep_spec, pkg.spec)
+    set_compiler_environment_variables(pkg, spack_env)
+    set_build_environment_variables(pkg, spack_env)
+    setup_module_variables_for_dag(pkg)
+
+    # Allow dependencies to modify the module
+    spec = pkg.spec
+    for dependency_spec in spec.traverse(root=False):
+        dpkg = dependency_spec.package
+        dpkg.setup_dependent_package(pkg.module, spec)
+
+    # Allow dependencies to set up environment as well
+    for dependency_spec in spec.traverse(root=False):
+        dpkg = dependency_spec.package
+        dpkg.setup_dependent_environment(spack_env, run_env, spec)
+
+    # Allow the package to apply some settings.
+    pkg.setup_environment(spack_env, run_env)
+
+    # Make sure nothing's strange about the Spack environment.
+    validate(spack_env, tty.warn)
+    spack_env.apply_modifications()
 
 
 def fork(pkg, function):
@@ -296,23 +343,23 @@ def child_fun():
            # do stuff
        build_env.fork(pkg, child_fun)
 
-    Forked processes are run with the build environemnt set up by
+    Forked processes are run with the build environment set up by
     spack.build_environment.  This allows package authors to have
-    full control over the environment, etc. without offecting
+    full control over the environment, etc. without affecting
     other builds that might be executed in the same spack call.
 
-    If something goes wrong, the child process is expected toprint
+    If something goes wrong, the child process is expected to print
     the error and the parent process will exit with error as
     well. If things go well, the child exits and the parent
     carries on.
     """
     try:
         pid = os.fork()
-    except OSError, e:
+    except OSError as e:
         raise InstallError("Unable to fork build process: %s" % e)
 
     if pid == 0:
-        # Give the child process the package's build environemnt.
+        # Give the child process the package's build environment.
         setup_package(pkg)
 
         try:
@@ -323,7 +370,7 @@ def child_fun():
             # which interferes with unit tests.
             os._exit(0)
 
-        except spack.error.SpackError, e:
+        except spack.error.SpackError as e:
             e.die()
 
         except:
@@ -338,8 +385,7 @@ def child_fun():
         # message.  Just make the parent exit with an error code.
         pid, returncode = os.waitpid(pid, 0)
         if returncode != 0:
-            raise InstallError("Installation process had nonzero exit code."
-                .format(str(returncode)))
+            raise InstallError("Installation process had nonzero exit code.".format(str(returncode)))
 
 
 class InstallError(spack.error.SpackError):

lib/spack/spack/cmd/create.py

@@ -208,7 +208,7 @@ def find_repository(spec, args):
     return repo
 
 
-def fetch_tarballs(url, name, args):
+def fetch_tarballs(url, name, version):
     """Try to find versions of the supplied archive by scraping the web.
 
     Prompts the user to select how many to download if many are found.
@@ -222,7 +222,7 @@ def fetch_tarballs(url, name, args):
     archives_to_fetch = 1
     if not versions:
         # If the fetch failed for some reason, revert to what the user provided
-        versions = { "version" : url }
+        versions = { version : url }
     elif len(versions) > 1:
         tty.msg("Found %s versions of %s:" % (len(versions), name),
                 *spack.cmd.elide_list(
@@ -256,7 +256,7 @@ def create(parser, args):
     tty.msg("Creating template for package %s" % name)
 
     # Fetch tarballs (prompting user if necessary)
-    versions, urls = fetch_tarballs(url, name, args)
+    versions, urls = fetch_tarballs(url, name, version)
 
     # Try to guess what configure system is used.
     guesser = ConfigureGuesser()

lib/spack/spack/cmd/diy.py

@@ -75,8 +75,8 @@ def diy(self, args):
                 edit_package(spec.name, spack.repo.first_repo(), None, True)
                 return
 
-        if not spec.version.concrete:
-            tty.die("spack diy spec must have a single, concrete version.")
+        if not spec.versions.concrete:
+            tty.die("spack diy spec must have a single, concrete version.  Did you forget a package version number?")
 
         spec.concretize()
         package = spack.repo.get(spec)

lib/spack/spack/cmd/module.py

@@ -80,7 +80,7 @@ def module_find(mtype, spec_array):
     if not os.path.isfile(mod.file_name):
         tty.die("No %s module is installed for %s" % (mtype, spec))
 
-    print mod.use_name
+    print(mod.use_name)
 
 
 def module_refresh():

lib/spack/spack/cmd/uninstall.py

@@ -22,6 +22,7 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
+from __future__ import print_function
 import sys
 import argparse
 
@@ -63,12 +64,12 @@ def uninstall(parser, args):
             matching_specs = spack.installed_db.query(spec)
             if not args.all and len(matching_specs) > 1:
                 tty.error("%s matches multiple packages:" % spec)
-                print
+                print()
                 display_specs(matching_specs, long=True)
-                print
-                print "You can either:"
-                print "  a) Use a more specific spec, or"
-                print "  b) use spack uninstall -a to uninstall ALL matching specs."
+                print()
+                print("You can either:")
+                print("  a) Use a more specific spec, or")
+                print("  b) use spack uninstall -a to uninstall ALL matching specs.")
                 sys.exit(1)
 
             if len(matching_specs) == 0:
@@ -79,7 +80,7 @@ def uninstall(parser, args):
                 try:
                     # should work if package is known to spack
                     pkgs.append(s.package)
-                except spack.repository.UnknownPackageError, e:
+                except spack.repository.UnknownPackageError as e:
                     # The package.py file has gone away -- but still
                     # want to uninstall.
                     spack.Package(s).do_uninstall(force=True)
@@ -94,11 +95,11 @@ def num_installed_deps(pkg):
         for pkg in pkgs:
             try:
                 pkg.do_uninstall(force=args.force)
-            except PackageStillNeededError, e:
+            except PackageStillNeededError as e:
                 tty.error("Will not uninstall %s" % e.spec.format("$_$@$%@$#", color=True))
-                print
-                print "The following packages depend on it:"
+                print('')
+                print("The following packages depend on it:")
                 display_specs(e.dependents, long=True)
-                print
-                print "You can use spack uninstall -f to force this action."
+                print('')
+                print("You can use spack uninstall -f to force this action.")
                 sys.exit(1)

lib/spack/spack/compilers/gcc.py

@@ -40,7 +40,8 @@ class Gcc(Compiler):
     fc_names = ['gfortran']
 
     # MacPorts builds gcc versions with prefixes and -mp-X.Y suffixes.
-    suffixes = [r'-mp-\d\.\d']
+    # Homebrew and Linuxes may build gcc with -X, -X.Y suffixes
+    suffixes = [r'-mp-\d\.\d', r'-\d\.\d', r'-\d']
 
     # Named wrapper links within spack.build_env_path
     link_paths = {'cc'  : 'gcc/gcc',

lib/spack/spack/concretize.py

@@ -51,10 +51,10 @@ class DefaultConcretizer(object):
     """
 
     def _valid_virtuals_and_externals(self, spec):
-        """Returns a list of spec/external-path pairs for both virtuals and externals
-           that can concretize this spec."""
-        # Get a list of candidate packages that could satisfy this spec
-        packages = []
+        """Returns a list of candidate virtual dep providers and external
+           packages that coiuld be used to concretize a spec."""
+        # First construct a list of concrete candidates to replace spec with.
+        candidates = [spec]
         if spec.virtual:
             providers = spack.repo.providers_for(spec)
             if not providers:
@@ -64,96 +64,72 @@ def _valid_virtuals_and_externals(self, spec):
             if not spec_w_preferred_providers:
                 spec_w_preferred_providers = spec
             provider_cmp = partial(spack.pkgsort.provider_compare, spec_w_preferred_providers.name, spec.name)
-            packages = sorted(providers, cmp=provider_cmp)
-        else:
-            packages = [spec]
+            candidates = sorted(providers, cmp=provider_cmp)
 
-        # For each candidate package, if it has externals add those to the candidates
-        # if it's not buildable, then only add the externals.
-        candidates = []
-        all_compilers = spack.compilers.all_compilers()
-        for pkg in packages:
-            externals = spec_externals(pkg)
-            buildable = is_spec_buildable(pkg)
-            if buildable:
-                candidates.append((pkg, None))
+        # For each candidate package, if it has externals, add those to the usable list.
+        # if it's not buildable, then *only* add the externals.
+        usable = []
+        for cspec in candidates:
+            if is_spec_buildable(cspec):
+                usable.append(cspec)
+            externals = spec_externals(cspec)
             for ext in externals:
-                if ext[0].satisfies(spec):
-                    candidates.append(ext)
-        if not candidates:
+                if ext.satisfies(spec):
+                    usable.append(ext)
+
+        # If nothing is in the usable list now, it's because we aren't
+        # allowed to build anything.
+        if not usable:
             raise NoBuildError(spec)
 
         def cmp_externals(a, b):
-            if a[0].name != b[0].name:
-                #We're choosing between different providers. Maintain order from above sort
+            if a.name != b.name:
+                # We're choosing between different providers, so
+                # maintain order from provider sort
                 return candidates.index(a) - candidates.index(b)
-            result = cmp_specs(a[0], b[0])
+
+            result = cmp_specs(a, b)
             if result != 0:
                 return result
-            if not a[1] and b[1]:
-                return 1
-            if not b[1] and a[1]:
-                return -1
-            return cmp(a[1], b[1])
 
-        candidates = sorted(candidates, cmp=cmp_externals)
-        return candidates
+            # prefer external packages to internal packages.
+            if a.external is None or b.external is None:
+                return -cmp(a.external, b.external)
+            else:
+                return cmp(a.external, b.external)
+
+        usable.sort(cmp=cmp_externals)
+        return usable
 
 
-    def concretize_virtual_and_external(self, spec):
-        """From a list of candidate virtual and external packages, concretize to one that
-           is ABI compatible with the rest of the DAG."""
+    def choose_virtual_or_external(self, spec):
+        """Given a list of candidate virtual and external packages, try to
+           find one that is most ABI compatible.
+        """
         candidates = self._valid_virtuals_and_externals(spec)
         if not candidates:
-            return False
+            return candidates
 
-        # Find the nearest spec in the dag that has a compiler.  We'll use that
-        # spec to test compiler compatibility.
-        other_spec = find_spec(spec, lambda(x): x.compiler)
-        if not other_spec:
-            other_spec = spec.root
+        # Find the nearest spec in the dag that has a compiler.  We'll
+        # use that spec to calibrate compiler compatibility.
+        abi_exemplar = find_spec(spec, lambda(x): x.compiler)
+        if not abi_exemplar:
+            abi_exemplar = spec.root
 
-        # Choose an ABI-compatible candidate, or the first match otherwise.
-        candidate = None
-        if other_spec:
-            candidate = next((c for c in candidates if spack.abi.compatible(c[0], other_spec)), None)
-            if not candidate:
-                # Try a looser ABI matching
-                candidate = next((c for c in candidates if spack.abi.compatible(c[0], other_spec, loose=True)), None)
-        if not candidate:
-            # No ABI matches. Pick the top choice based on the orignal preferences.
-            candidate = candidates[0]
-        candidate_spec = candidate[0]
-        external = candidate[1]
-        changed = False
+        # Make a list including ABI compatibility of specs with the exemplar.
+        strict = [spack.abi.compatible(c, abi_exemplar) for c in candidates]
+        loose  = [spack.abi.compatible(c, abi_exemplar, loose=True) for c in candidates]
+        keys = zip(strict, loose, candidates)
 
-        # If we're external then trim the dependencies
-        if external:
-            if (spec.dependencies):
-                changed = True
-            spec.dependencies = DependencyMap()
-            candidate_spec.dependencies = DependencyMap()
+        # Sort candidates from most to least compatibility.
+        # Note:
+        #   1. We reverse because True > False.
+        #   2. Sort is stable, so c's keep their order.
+        keys.sort(key=lambda k:k[:2], reverse=True)
 
-        def fequal(candidate_field, spec_field):
-            return (not candidate_field) or (candidate_field == spec_field)
-        if (fequal(candidate_spec.name, spec.name) and
-            fequal(candidate_spec.versions, spec.versions) and
-            fequal(candidate_spec.compiler, spec.compiler) and
-            fequal(candidate_spec.architecture, spec.architecture) and
-            fequal(candidate_spec.dependencies, spec.dependencies) and
-            fequal(candidate_spec.variants, spec.variants) and
-            fequal(external, spec.external)):
-            return changed
-
-        # Refine this spec to the candidate.
-        if spec.virtual:
-            spec._replace_with(candidate_spec)
-            changed = True
-        if spec._dup(candidate_spec, deps=False, cleardeps=False):
-            changed = True
-        spec.external = external
-
-        return changed
+        # Pull the candidates back out and return them in order
+        candidates = [c for s,l,c in keys]
+        return candidates
 
 
     def concretize_version(self, spec):
@@ -183,6 +159,10 @@ def concretize_version(self, spec):
              if any(v.satisfies(sv) for sv in spec.versions)],
             cmp=cmp_versions)
 
+        def prefer_key(v):
+            return pkg.versions.get(Version(v)).get('preferred', False)
+        valid_versions.sort(key=prefer_key, reverse=True)
+
         if valid_versions:
             spec.versions = ver([valid_versions[0]])
         else:
@@ -238,7 +218,7 @@ def concretize_variants(self, spec):
            the default variants from the package specification.
         """
         changed = False
-        for name, variant in spec.package.variants.items():
+        for name, variant in spec.package_class.variants.items():
             if name not in spec.variants:
                 spec.variants[name] = spack.spec.VariantSpec(name, variant.default)
                 changed = True
@@ -265,7 +245,7 @@ def concretize_compiler(self, spec):
             return False
 
         #Find the another spec that has a compiler, or the root if none do
-        other_spec = find_spec(spec, lambda(x) : x.compiler)
+        other_spec = spec if spec.compiler else find_spec(spec, lambda(x) : x.compiler)
         if not other_spec:
             other_spec = spec.root
         other_compiler = other_spec.compiler
@@ -312,7 +292,7 @@ def find_spec(spec, condition):
     if condition(spec):
         return spec
 
-    return None   # Nohting matched the condition.
+    return None   # Nothing matched the condition.
 
 
 def cmp_specs(lhs, rhs):

lib/spack/spack/config.py

@@ -237,7 +237,29 @@
                                 'type' : 'object',
                                 'default' : {},
                             }
-                        },},},},},}
+                        },},},},},},
+    'modules': {
+        '$schema': 'http://json-schema.org/schema#',
+        'title': 'Spack module file configuration file schema',
+        'type': 'object',
+        'additionalProperties': False,
+        'patternProperties': {
+            r'modules:?': {
+                'type': 'object',
+                'default': {},
+                'additionalProperties': False,
+                'properties': {
+                    'enable': {
+                        'type': 'array',
+                        'default': [],
+                        'items': {
+                            'type': 'string'
+                        }
+                    }
+                }
+            },
+        },
+    },
 }
 
 """OrderedDict of config scopes keyed by name.
@@ -405,11 +427,11 @@ def _read_config_file(filename, schema):
             validate_section(data, schema)
         return data
 
-    except MarkedYAMLError, e:
+    except MarkedYAMLError as e:
         raise ConfigFileError(
             "Error parsing yaml%s: %s" % (str(e.context_mark), e.problem))
 
-    except IOError, e:
+    except IOError as e:
         raise ConfigFileError(
             "Error reading configuration file %s: %s" % (filename, str(e)))
 
@@ -539,22 +561,25 @@ def print_section(section):
 
 
 def spec_externals(spec):
-    """Return a list of spec, directory pairs for each external location for spec"""
+    """Return a list of external specs (with external directory path filled in),
+       one for each known external installation."""
     allpkgs = get_config('packages')
     name = spec.name
-    spec_locations = []
 
+    external_specs = []
     pkg_paths = allpkgs.get(name, {}).get('paths', None)
     if not pkg_paths:
         return []
 
-    for pkg,path in pkg_paths.iteritems():
-        if not spec.satisfies(pkg):
-            continue
+    for external_spec, path in pkg_paths.iteritems():
         if not path:
+            # skip entries without paths (avoid creating extra Specs)
             continue
-        spec_locations.append( (spack.spec.Spec(pkg), path) )
-    return spec_locations
+
+        external_spec = spack.spec.Spec(external_spec, external=path)
+        if external_spec.satisfies(spec):
+            external_specs.append(external_spec)
+    return external_specs
 
 
 def is_spec_buildable(spec):

lib/spack/spack/directory_layout.py

@@ -150,7 +150,7 @@ def remove_install_directory(self, spec):
         if os.path.exists(path):
             try:
                 shutil.rmtree(path)
-            except exceptions.OSError, e:
+            except exceptions.OSError as e:
                 raise RemoveFailedError(spec, path, e)
 
         path = os.path.dirname(path)

lib/spack/spack/environment.py

@@ -0,0 +1,252 @@
+import os
+import os.path
+import collections
+import inspect
+
+
+class NameModifier(object):
+    def __init__(self, name, **kwargs):
+        self.name = name
+        self.args = {'name': name}
+        self.args.update(kwargs)
+
+
+class NameValueModifier(object):
+    def __init__(self, name, value, **kwargs):
+        self.name = name
+        self.value = value
+        self.args = {'name': name, 'value': value}
+        self.args.update(kwargs)
+
+
+class SetEnv(NameValueModifier):
+    def execute(self):
+        os.environ[self.name] = str(self.value)
+
+
+class UnsetEnv(NameModifier):
+    def execute(self):
+        os.environ.pop(self.name, None)  # Avoid throwing if the variable was not set
+
+
+class SetPath(NameValueModifier):
+    def execute(self):
+        string_path = concatenate_paths(self.value)
+        os.environ[self.name] = string_path
+
+
+class AppendPath(NameValueModifier):
+    def execute(self):
+        environment_value = os.environ.get(self.name, '')
+        directories = environment_value.split(':') if environment_value else []
+        directories.append(os.path.normpath(self.value))
+        os.environ[self.name] = ':'.join(directories)
+
+
+class PrependPath(NameValueModifier):
+    def execute(self):
+        environment_value = os.environ.get(self.name, '')
+        directories = environment_value.split(':') if environment_value else []
+        directories = [os.path.normpath(self.value)] + directories
+        os.environ[self.name] = ':'.join(directories)
+
+
+class RemovePath(NameValueModifier):
+    def execute(self):
+        environment_value = os.environ.get(self.name, '')
+        directories = environment_value.split(':') if environment_value else []
+        directories = [os.path.normpath(x) for x in directories if x != os.path.normpath(self.value)]
+        os.environ[self.name] = ':'.join(directories)
+
+
+class EnvironmentModifications(object):
+    """
+    Keeps track of requests to modify the current environment.
+
+    Each call to a method to modify the environment stores the extra information on the caller in the request:
+    - 'filename' : filename of the module where the caller is defined
+    - 'lineno': line number where the request occurred
+    - 'context' : line of code that issued the request that failed
+    """
+
+    def __init__(self, other=None):
+        """
+        Initializes a new instance, copying commands from other if it is not None
+
+        Args:
+            other: another instance of EnvironmentModifications from which (optional)
+        """
+        self.env_modifications = []
+        if other is not None:
+            self.extend(other)
+
+    def __iter__(self):
+        return iter(self.env_modifications)
+
+    def __len__(self):
+        return len(self.env_modifications)
+
+    def extend(self, other):
+        self._check_other(other)
+        self.env_modifications.extend(other.env_modifications)
+
+    @staticmethod
+    def _check_other(other):
+        if not isinstance(other, EnvironmentModifications):
+            raise TypeError('other must be an instance of EnvironmentModifications')
+
+    def _get_outside_caller_attributes(self):
+        stack = inspect.stack()
+        try:
+            _, filename, lineno, _, context, index = stack[2]
+            context = context[index].strip()
+        except Exception:
+            filename, lineno, context = 'unknown file', 'unknown line', 'unknown context'
+        args = {
+            'filename': filename,
+            'lineno': lineno,
+            'context': context
+        }
+        return args
+
+    def set(self, name, value, **kwargs):
+        """
+        Stores in the current object a request to set an environment variable
+
+        Args:
+            name: name of the environment variable to be set
+            value: value of the environment variable
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = SetEnv(name, value, **kwargs)
+        self.env_modifications.append(item)
+
+    def unset(self, name, **kwargs):
+        """
+        Stores in the current object a request to unset an environment variable
+
+        Args:
+            name: name of the environment variable to be set
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = UnsetEnv(name, **kwargs)
+        self.env_modifications.append(item)
+
+    def set_path(self, name, elts, **kwargs):
+        """
+        Stores a request to set a path generated from a list.
+
+        Args:
+            name: name o the environment variable to be set.
+            elts: elements of the path to set.
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = SetPath(name, elts, **kwargs)
+        self.env_modifications.append(item)
+
+    def append_path(self, name, path, **kwargs):
+        """
+        Stores in the current object a request to append a path to a path list
+
+        Args:
+            name: name of the path list in the environment
+            path: path to be appended
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = AppendPath(name, path, **kwargs)
+        self.env_modifications.append(item)
+
+    def prepend_path(self, name, path, **kwargs):
+        """
+        Same as `append_path`, but the path is pre-pended
+
+        Args:
+            name: name of the path list in the environment
+            path: path to be pre-pended
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = PrependPath(name, path, **kwargs)
+        self.env_modifications.append(item)
+
+    def remove_path(self, name, path, **kwargs):
+        """
+        Stores in the current object a request to remove a path from a path list
+
+        Args:
+            name: name of the path list in the environment
+            path: path to be removed
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = RemovePath(name, path, **kwargs)
+        self.env_modifications.append(item)
+
+    def group_by_name(self):
+        """
+        Returns a dict of the modifications grouped by variable name
+
+        Returns:
+            dict mapping the environment variable name to the modifications to be done on it
+        """
+        modifications = collections.defaultdict(list)
+        for item in self:
+            modifications[item.name].append(item)
+        return modifications
+
+    def clear(self):
+        """
+        Clears the current list of modifications
+        """
+        self.env_modifications.clear()
+
+    def apply_modifications(self):
+        """
+        Applies the modifications and clears the list
+        """
+        modifications = self.group_by_name()
+        # Apply the modifications to the environment variables one variable at a time
+        for name, actions in sorted(modifications.items()):
+            for x in actions:
+                x.execute()
+
+
+def concatenate_paths(paths):
+    """
+    Concatenates an iterable of paths into a  string of column separated paths
+
+    Args:
+        paths: iterable of paths
+
+    Returns:
+        string
+    """
+    return ':'.join(str(item) for item in paths)
+
+
+def set_or_unset_not_first(variable, changes, errstream):
+    """
+    Check if we are going to set or unset something after other modifications have already been requested
+    """
+    indexes = [ii for ii, item in enumerate(changes) if ii != 0 and type(item) in [SetEnv, UnsetEnv]]
+    if indexes:
+        good = '\t    \t{context} at {filename}:{lineno}'
+        nogood = '\t--->\t{context} at {filename}:{lineno}'
+        errstream('Suspicious requests to set or unset the variable \'{var}\' found'.format(var=variable))
+        for ii, item in enumerate(changes):
+            print_format = nogood if ii in indexes else good
+            errstream(print_format.format(**item.args))
+
+
+def validate(env, errstream):
+    """
+    Validates the environment modifications to check for the presence of suspicious patterns. Prompts a warning for
+    everything that was found
+
+    Current checks:
+    - set or unset variables after other changes on the same variable
+
+    Args:
+        env: list of environment modifications
+    """
+    modifications = env.group_by_name()
+    for variable, list_of_changes in sorted(modifications.items()):
+        set_or_unset_not_first(variable, list_of_changes, errstream)

lib/spack/spack/modules.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
 ##############################################################################
-"""This module contains code for creating environment modules, which
-can include dotkits, tcl modules, lmod, and others.
+"""
+This module contains code for creating environment modules, which can include dotkits, tcl modules, lmod, and others.
 
-The various types of modules are installed by post-install hooks and
-removed after an uninstall by post-uninstall hooks.  This class
-consolidates the logic for creating an abstract description of the
-information that module systems need.  Currently that includes a
-number of directories to be appended to paths in the user's environment:
+The various types of modules are installed by post-install hooks and removed after an uninstall by post-uninstall hooks.
+This class consolidates the logic for creating an abstract description of the information that module systems need.
+Currently that includes a number of directories to be appended to paths in the user's environment:
 
   * /bin directories to be appended to PATH
   * /lib* directories for LD_LIBRARY_PATH
@@ -37,30 +35,30 @@
   * /man* and /share/man* directories for MANPATH
   * the package prefix for CMAKE_PREFIX_PATH
 
-This module also includes logic for coming up with unique names for
-the module files so that they can be found by the various
-shell-support files in $SPACK/share/spack/setup-env.*.
+This module also includes logic for coming up with unique names for the module files so that they can be found by the
+various shell-support files in $SPACK/share/spack/setup-env.*.
 
-Each hook in hooks/ implements the logic for writing its specific type
-of module file.
+Each hook in hooks/ implements the logic for writing its specific type of module file.
 """
-__all__ = ['EnvModule', 'Dotkit', 'TclModule']
-
 import os
+import os.path
 import re
-import textwrap
 import shutil
-from glob import glob
+import textwrap
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import join_path, mkdirp
-
 import spack
+import spack.config
+from llnl.util.filesystem import join_path, mkdirp
+from spack.environment import *
 
-"""Registry of all types of modules.  Entries created by EnvModule's
-   metaclass."""
+__all__ = ['EnvModule', 'Dotkit', 'TclModule']
+
+# Registry of all types of modules.  Entries created by EnvModule's metaclass
 module_types = {}
 
+CONFIGURATION = spack.config.get_config('modules')
+
 
 def print_help():
     """For use by commands to tell user how to activate shell support."""
@@ -79,75 +77,76 @@ def print_help():
             "")
 
 
+def inspect_path(prefix):
+    """
+    Inspects the prefix of an installation to search for common layouts. Issues a request to modify the environment
+    accordingly when an item is found.
+
+    Args:
+        prefix: prefix of the installation
+
+    Returns:
+        instance of EnvironmentModifications containing the requested modifications
+    """
+    env = EnvironmentModifications()
+    # Inspect the prefix to check for the existence of common directories
+    prefix_inspections = {
+        'bin': ('PATH',),
+        'man': ('MANPATH',),
+        'lib': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'),
+        'lib64': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'),
+        'include': ('CPATH',)
+    }
+    for attribute, variables in prefix_inspections.items():
+        expected = getattr(prefix, attribute)
+        if os.path.isdir(expected):
+            for variable in variables:
+                env.prepend_path(variable, expected)
+    # PKGCONFIG
+    for expected in (join_path(prefix.lib, 'pkgconfig'), join_path(prefix.lib64, 'pkgconfig')):
+        if os.path.isdir(expected):
+            env.prepend_path('PKG_CONFIG_PATH', expected)
+    # CMake related variables
+    env.prepend_path('CMAKE_PREFIX_PATH', prefix)
+    return env
+
+
 class EnvModule(object):
     name = 'env_module'
+    formats = {}
 
     class __metaclass__(type):
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
-            if cls.name != 'env_module':
+            if cls.name != 'env_module' and cls.name in CONFIGURATION['enable']:
                 module_types[cls.name] = cls
 
-
     def __init__(self, spec=None):
-        # category in the modules system
-        # TODO: come up with smarter category names.
-        self.category = "spack"
-
-        # Descriptions for the module system's UI
-        self.short_description = ""
-        self.long_description = ""
-
-        # dict pathname -> list of directories to be prepended to in
-        # the module file.
-        self._paths = None
         self.spec = spec
+        self.pkg = spec.package  # Just stored for convenience
+
+        # short description default is just the package + version
+        # packages can provide this optional attribute
+        self.short_description = spec.format("$_ $@")
+        if hasattr(self.pkg, 'short_description'):
+            self.short_description = self.pkg.short_description
+
+        # long description is the docstring with reduced whitespace.
+        self.long_description = None
+        if self.spec.package.__doc__:
+            self.long_description = re.sub(r'\s+', ' ', self.spec.package.__doc__)
 
 
     @property
-    def paths(self):
-        if self._paths is None:
-            self._paths = {}
-
-            def add_path(path_name, directory):
-                path = self._paths.setdefault(path_name, [])
-                path.append(directory)
-
-            # Add paths if they exist.
-            for var, directory in [
-                    ('PATH', self.spec.prefix.bin),
-                    ('MANPATH', self.spec.prefix.man),
-                    ('MANPATH', self.spec.prefix.share_man),
-                    ('LIBRARY_PATH', self.spec.prefix.lib),
-                    ('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'))]:
-
-                if os.path.isdir(directory):
-                    add_path(var, directory)
-
-            # Add python path unless it's an actual python installation
-            # TODO: is there a better way to do this?
-            if self.spec.name != 'python':
-                site_packages = glob(join_path(self.spec.prefix.lib, "python*/site-packages"))
-                if site_packages:
-                    add_path('PYTHONPATH', site_packages[0])
-
-            if self.spec.package.extends(spack.spec.Spec('ruby')):
-              add_path('GEM_PATH', self.spec.prefix)
-
-            # short description is just the package + version
-            # TODO: maybe packages can optionally provide it.
-            self.short_description = self.spec.format("$_ $@")
-
-            # long description is the docstring with reduced whitespace.
-            if self.spec.package.__doc__:
-                self.long_description = re.sub(r'\s+', ' ', self.spec.package.__doc__)
-
-        return self._paths
+    def category(self):
+        # Anything defined at the package level takes precedence
+        if hasattr(self.pkg, 'category'):
+            return self.pkg.category
+        # Extensions
+        for extendee in self.pkg.extendees:
+            return '{extendee} extension'.format(extendee=extendee)
+        # Not very descriptive fallback
+        return 'spack installed package'
 
 
     def write(self):
@@ -156,18 +155,41 @@ def write(self):
         if not os.path.exists(module_dir):
             mkdirp(module_dir)
 
-        # If there are no paths, no need for a dotkit.
-        if not self.paths:
+        # Environment modifications guessed by inspecting the
+        # installation prefix
+        env = inspect_path(self.spec.prefix)
+
+        # Let the extendee modify their extensions before asking for
+        # package-specific modifications
+        spack_env = EnvironmentModifications()
+        for item in self.pkg.extendees:
+            package = self.spec[item].package
+            package.setup_dependent_package(self.pkg.module, self.spec)
+            package.setup_dependent_environment(spack_env, env, self.spec)
+
+        # Package-specific environment modifications
+        self.spec.package.setup_environment(spack_env, env)
+
+        # TODO : implement site-specific modifications and filters
+        if not env:
             return
 
         with open(self.file_name, 'w') as f:
-            self._write(f)
+            self.write_header(f)
+            for line in self.process_environment_command(env):
+                f.write(line)
 
-
-    def _write(self, stream):
-        """To be implemented by subclasses."""
+    def write_header(self, stream):
         raise NotImplementedError()
 
+    def process_environment_command(self, env):
+        for command in env:
+            try:
+                yield self.formats[type(command)].format(**command.args)
+            except KeyError:
+                tty.warn('Cannot handle command of type {command} : skipping request'.format(command=type(command)))
+                tty.warn('{context} at {filename}:{lineno}'.format(**command.args))
+
 
     @property
     def file_name(self):
@@ -175,14 +197,12 @@ def file_name(self):
            where this module lives."""
         raise NotImplementedError()
 
-
     @property
     def use_name(self):
         """Subclasses should implement this to return the name the
            module command uses to refer to the package."""
         raise NotImplementedError()
 
-
     def remove(self):
         mod_file = self.file_name
         if os.path.exists(mod_file):
@@ -193,19 +213,23 @@ class Dotkit(EnvModule):
     name = 'dotkit'
     path = join_path(spack.share_path, "dotkit")
 
+    formats = {
+        PrependPath: 'dk_alter {name} {value}\n',
+        SetEnv: 'dk_setenv {name} {value}\n'
+    }
+
     @property
     def file_name(self):
-        return join_path(Dotkit.path, self.spec.architecture,
-                         '%s.dk' % self.use_name)
+        return join_path(Dotkit.path, self.spec.architecture, '%s.dk' % self.use_name)
 
     @property
     def use_name(self):
       return "%s-%s-%s-%s-%s" % (self.spec.name, self.spec.version,
                                  self.spec.compiler.name,
-                                 self.spec.compiler.version, 
+                                 self.spec.compiler.version,
                                  self.spec.dag_hash())
 
-    def _write(self, dk_file):
+    def write_header(self, dk_file):
         # Category
         if self.category:
             dk_file.write('#c %s\n' % self.category)
@@ -219,50 +243,41 @@ def _write(self, dk_file):
             for line in textwrap.wrap(self.long_description, 72):
                 dk_file.write("#h %s\n" % line)
 
-        # Path alterations
-        for var, dirs in self.paths.items():
-            for directory in dirs:
-                dk_file.write("dk_alter %s %s\n" % (var, directory))
-
-        # Let CMake find this package.
-        dk_file.write("dk_alter CMAKE_PREFIX_PATH %s\n" % self.spec.prefix)
-
 
 class TclModule(EnvModule):
     name = 'tcl'
     path = join_path(spack.share_path, "modules")
 
+    formats = {
+        PrependPath: 'prepend-path {name} \"{value}\"\n',
+        AppendPath: 'append-path {name} \"{value}\"\n',
+        RemovePath: 'remove-path {name} \"{value}\"\n',
+        SetEnv: 'setenv {name} \"{value}\"\n',
+        UnsetEnv: 'unsetenv {name}\n'
+    }
+
     @property
     def file_name(self):
         return join_path(TclModule.path, self.spec.architecture, self.use_name)
 
-
     @property
     def use_name(self):
       return "%s-%s-%s-%s-%s" % (self.spec.name, self.spec.version,
                                  self.spec.compiler.name,
-                                 self.spec.compiler.version, 
+                                 self.spec.compiler.version,
                                  self.spec.dag_hash())
 
-
-    def _write(self, m_file):
-        # TODO: cateogry?
-        m_file.write('#%Module1.0\n')
-
+    def write_header(self, module_file):
+        # TCL Modulefile header
+        module_file.write('#%Module1.0\n')
+        # TODO : category ?
         # Short description
         if self.short_description:
-            m_file.write('module-whatis \"%s\"\n\n' % self.short_description)
+            module_file.write('module-whatis \"%s\"\n\n' % self.short_description)
 
         # Long description
         if self.long_description:
-            m_file.write('proc ModulesHelp { } {\n')
+            module_file.write('proc ModulesHelp { } {\n')
             doc = re.sub(r'"', '\"', self.long_description)
-            m_file.write("puts stderr \"%s\"\n" % doc)
-            m_file.write('}\n\n')
-
-        # Path alterations
-        for var, dirs in self.paths.items():
-            for directory in dirs:
-                m_file.write("prepend-path %s \"%s\"\n" % (var, directory))
-
-        m_file.write("prepend-path CMAKE_PREFIX_PATH \"%s\"\n" % self.spec.prefix)
+            module_file.write("puts stderr \"%s\"\n" % doc)
+            module_file.write('}\n\n')

lib/spack/spack/package.py

@@ -34,44 +34,34 @@
 README.
 """
 import os
-import errno
 import re
-import shutil
-import time
-import itertools
-import subprocess
-import platform as py_platform
-import multiprocessing
-from urlparse import urlparse, urljoin
 import textwrap
-from StringIO import StringIO
-import shutil
-import sys
-import string
+import time
+import glob
 
 import llnl.util.tty as tty
-from llnl.util.tty.log import log_output
-from llnl.util.link_tree import LinkTree
-from llnl.util.filesystem import *
-from llnl.util.lang import *
-
 import spack
-import spack.error
-import spack.compilers
-import spack.mirror
-import spack.hooks
-import spack.directives
-import spack.repository
 import spack.build_environment
+import spack.compilers
+import spack.directives
+import spack.error
+import spack.fetch_strategy as fs
+import spack.hooks
+import spack.mirror
+import spack.repository
 import spack.url
 import spack.util.web
-import spack.fetch_strategy as fs
-from spack.version import *
+from StringIO import StringIO
+from llnl.util.filesystem import *
+from llnl.util.lang import *
+from llnl.util.link_tree import LinkTree
+from llnl.util.tty.log import log_output
 from spack.stage import Stage, ResourceStage, StageComposite
-from spack.util.compression import allowed_archive, extension
-from spack.util.executable import ProcessError, which
+from spack.util.compression import allowed_archive
 from spack.util.environment import dump_environment
-from spack import directory_layout
+from spack.util.executable import ProcessError
+from spack.version import *
+from urlparse import urlparse
 
 """Allowed URL schemes for spack packages."""
 _ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"]
@@ -322,6 +312,18 @@ class SomePackage(Package):
     """Most packages are NOT extendable.  Set to True if you want extensions."""
     extendable = False
 
+    """List of prefix-relative file paths (or a single path). If these do
+       not exist after install, or if they exist but are not files,
+       sanity checks fail.
+    """
+    sanity_check_is_file = []
+
+    """List of prefix-relative directory paths (or a single path). If
+       these do not exist after install, or if they exist but are not
+       directories, sanity checks will fail.
+    """
+    sanity_check_is_dir = []
+
 
     def __init__(self, spec):
         # this determines how the package should be built.
@@ -919,12 +921,11 @@ def build_process():
 
                     # Ensure that something was actually installed.
                     if 'install' in self.install_phases:
-                        self._sanity_check_install()
+                        self.sanity_check_prefix()
 
 
                     # Copy provenance into the install directory on success
                     if 'provenance' in self.install_phases:
-
                         log_install_path = spack.install_layout.build_log_path(self.spec)
                         env_install_path = spack.install_layout.build_env_path(self.spec)
                         packages_dir = spack.install_layout.build_packages_path(self.spec)
@@ -985,7 +986,21 @@ def build_process():
         spack.hooks.post_install(self)
 
 
-    def _sanity_check_install(self):
+    def sanity_check_prefix(self):
+        """This function checks whether install succeeded."""
+        def check_paths(path_list, filetype, predicate):
+            if isinstance(path_list, basestring):
+                path_list = [path_list]
+
+            for path in path_list:
+                abs_path = os.path.join(self.prefix, path)
+                if not predicate(abs_path):
+                    raise InstallError("Install failed for %s. No such %s in prefix: %s"
+                                       % (self.name, filetype, path))
+
+        check_paths(self.sanity_check_is_file, 'file', os.path.isfile)
+        check_paths(self.sanity_check_is_dir, 'directory', os.path.isdir)
+
         installed = set(os.listdir(self.prefix))
         installed.difference_update(spack.install_layout.hidden_file_paths)
         if not installed:
@@ -1015,38 +1030,127 @@ def module(self):
         return __import__(self.__class__.__module__,
                           fromlist=[self.__class__.__name__])
 
+    def setup_environment(self, spack_env, run_env):
+        """Set up the compile and runtime environemnts for a package.
 
-    def setup_dependent_environment(self, module, spec, dependent_spec):
-        """Called before the install() method of dependents.
+        `spack_env` and `run_env` are `EnvironmentModifications`
+        objects.  Package authors can call methods on them to alter
+        the environment within Spack and at runtime.
+
+        Both `spack_env` and `run_env` are applied within the build
+        process, before this package's `install()` method is called.
+
+        Modifications in `run_env` will *also* be added to the
+        generated environment modules for this package.
 
         Default implementation does nothing, but this can be
-        overridden by an extendable package to set up the install
-        environment for its extensions.  This is useful if there are
-        some common steps to installing all extensions for a
-        certain package.
+        overridden if the package needs a particular environment.
 
-        Some examples:
+        Examples:
 
-        1. Installing python modules generally requires PYTHONPATH to
-           point to the lib/pythonX.Y/site-packages directory in the
-           module's install prefix.  This could set that variable.
+            1. Qt extensions need `QTDIR` set.
 
-        2. Extensions often need to invoke the 'python' interpreter
-           from the Python installation being extended.  This routine can
-           put a 'python' Execuable object in the module scope for the
-           extension package to simplify extension installs.
+        Args:
+            spack_env (EnvironmentModifications): list of
+                modifications to be applied when this package is built
+                within Spack.
 
-        3. A lot of Qt extensions need QTDIR set.  This can be used to do that.
+            run_env (EnvironmentModifications): list of environment
+                changes to be applied when this package is run outside
+                of Spack.
 
         """
         pass
 
 
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        """Set up the environment of packages that depend on this one.
+
+        This is similar to `setup_environment`, but it is used to
+        modify the compile and runtime environments of packages that
+        *depend* on this one. This gives packages like Python and
+        others that follow the extension model a way to implement
+        common environment or compile-time settings for dependencies.
+
+        By default, this delegates to self.setup_environment()
+
+        Example :
+
+            1. Installing python modules generally requires
+              `PYTHONPATH` to point to the lib/pythonX.Y/site-packages
+              directory in the module's install prefix.  This could
+              set that variable.
+
+        Args:
+
+            spack_env (EnvironmentModifications): list of
+                modifications to be applied when the dependent package
+                is bulit within Spack.
+
+            run_env (EnvironmentModifications): list of environment
+                changes to be applied when the dependent package is
+                run outside of Spack.
+
+            dependent_spec (Spec): The spec of the dependent package
+                about to be built. This allows the extendee (self) to
+                query the dependent's state. Note that *this*
+                package's spec is available as `self.spec`.
+
+        This is useful if there are some common steps to installing
+        all extensions for a certain package.
+
+        """
+        self.setup_environment(spack_env, run_env)
+
+
+    def setup_dependent_package(self, module, dependent_spec):
+        """Set up Python module-scope variables for dependent packages.
+
+        Called before the install() method of dependents.
+
+        Default implementation does nothing, but this can be
+        overridden by an extendable package to set up the module of
+        its extensions. This is useful if there are some common steps
+        to installing all extensions for a certain package.
+
+        Example :
+
+            1. Extensions often need to invoke the `python`
+               interpreter from the Python installation being
+               extended.  This routine can put a 'python' Executable
+               object in the module scope for the extension package to
+               simplify extension installs.
+
+            2. MPI compilers could set some variables in the
+               dependent's scope that point to `mpicc`, `mpicxx`,
+               etc., allowing them to be called by common names
+               regardless of which MPI is used.
+
+            3. BLAS/LAPACK implementations can set some variables
+               indicating the path to their libraries, since these
+               paths differ by BLAS/LAPACK implementation.
+
+        Args:
+
+            module (module): The Python `module` object of the
+                dependent package. Packages can use this to set
+                module-scope variables for the dependent to use.
+
+            dependent_spec (Spec): The spec of the dependent package
+                about to be built. This allows the extendee (self) to
+                query the dependent's state.  Note that *this*
+                package's spec is available as `self.spec`.
+
+        This is useful if there are some common steps to installing
+        all extensions for a certain package.
+
+        """
+        pass
+
     def install(self, spec, prefix):
         """Package implementations override this with their own build configuration."""
         raise InstallError("Package %s provides no install method!" % self.name)
 
-
     def do_uninstall(self, force=False):
         if not self.installed:
             raise InstallError(str(self.spec) + " is not installed.")
@@ -1250,6 +1354,27 @@ def rpath_args(self):
         return " ".join("-Wl,-rpath,%s" % p for p in self.rpath)
 
 
+def install_dependency_symlinks(pkg, spec, prefix):
+    """Execute a dummy install and flatten dependencies"""
+    flatten_dependencies(spec, prefix)
+
+def flatten_dependencies(spec, flat_dir):
+    """Make each dependency of spec present in dir via symlink."""
+    for dep in spec.traverse(root=False):
+        name = dep.name
+
+        dep_path = spack.install_layout.path_for_spec(dep)
+        dep_files = LinkTree(dep_path)
+
+        os.mkdir(flat_dir+'/'+name)
+
+        conflict = dep_files.find_conflict(flat_dir+'/'+name)
+        if conflict:
+            raise DependencyConflictError(conflict)
+
+        dep_files.merge(flat_dir+'/'+name)
+
+
 def validate_package_url(url_string):
     """Determine whether spack can handle a particular URL or not."""
     url = urlparse(url_string)
@@ -1467,6 +1592,10 @@ def __init__(self, message, long_msg=None):
         super(InstallError, self).__init__(message, long_msg)
 
 
+class ExternalPackageError(InstallError):
+    """Raised by install() when a package is only for external use."""
+
+
 class PackageStillNeededError(InstallError):
     """Raised when package is still needed by another on uninstall."""
     def __init__(self, spec, dependents):
@@ -1517,3 +1646,11 @@ def __init__(self, path):
 class ActivationError(ExtensionError):
     def __init__(self, msg, long_msg=None):
         super(ActivationError, self).__init__(msg, long_msg)
+
+
+class DependencyConflictError(spack.error.SpackError):
+    """Raised when the dependencies cannot be flattened as asked for."""
+    def __init__(self, conflict):
+        super(DependencyConflictError, self).__init__(
+            "%s conflicts with another file in the flattened directory." %(
+                conflict))

lib/spack/spack/repository.py

@@ -316,6 +316,11 @@ def get(self, spec, new=False):
         return self.repo_for_pkg(spec).get(spec)
 
 
+    def get_pkg_class(self, pkg_name):
+        """Find a class for the spec's package and return the class object."""
+        return self.repo_for_pkg(pkg_name).get_pkg_class(pkg_name)
+
+
     @_autospec
     def dump_provenance(self, spec, path):
         """Dump provenance information for a spec to a particular path.
@@ -550,7 +555,7 @@ def get(self, spec, new=False):
 
         key = hash(spec)
         if new or key not in self._instances:
-            package_class = self._get_pkg_class(spec.name)
+            package_class = self.get_pkg_class(spec.name)
             try:
                 copy = spec.copy() # defensive copy.  Package owns its spec.
                 self._instances[key] = package_class(copy)
@@ -715,7 +720,7 @@ def _get_pkg_module(self, pkg_name):
         return self._modules[pkg_name]
 
 
-    def _get_pkg_class(self, pkg_name):
+    def get_pkg_class(self, pkg_name):
         """Get the class for the package out of its module.
 
         First loads (or fetches from cache) a module for the

lib/spack/spack/spec.py

@@ -353,7 +353,7 @@ def constrain(self, other):
     @property
     def concrete(self):
         return self.spec._concrete or all(
-            v in self for v in self.spec.package.variants)
+            v in self for v in self.spec.package_class.variants)
 
 
     def copy(self):
@@ -418,9 +418,11 @@ def __init__(self, spec_like, *dep_like, **kwargs):
         # cases we've read them from a file want to assume normal.
         # This allows us to manipulate specs that Spack doesn't have
         # package.py files for.
-        self._normal = kwargs.get('normal', False)
+        self._normal   = kwargs.get('normal', False)
         self._concrete = kwargs.get('concrete', False)
-        self.external = None
+
+        # Allow a spec to be constructed with an external path.
+        self.external  = kwargs.get('external', None)
 
         # This allows users to construct a spec DAG with literals.
         # Note that given two specs a and b, Spec(a) copies a, but
@@ -498,6 +500,14 @@ def package(self):
         return spack.repo.get(self)
 
 
+    @property
+    def package_class(self):
+        """Internal package call gets only the class object for a package.
+           Use this to just get package metadata.
+        """
+        return spack.repo.get_pkg_class(self.name)
+
+
     @property
     def virtual(self):
         """Right now, a spec is virtual if no package exists with its name.
@@ -786,8 +796,30 @@ def _replace_with(self, concrete):
         """Replace this virtual spec with a concrete spec."""
         assert(self.virtual)
         for name, dependent in self.dependents.items():
+            # remove self from all dependents.
             del dependent.dependencies[self.name]
-            dependent._add_dependency(concrete)
+
+            # add the replacement, unless it is already a dep of dependent.
+            if concrete.name not in dependent.dependencies:
+                dependent._add_dependency(concrete)
+
+
+    def _replace_node(self, replacement):
+        """Replace this spec with another.
+
+        Connects all dependents of this spec to its replacement, and
+        disconnects this spec from any dependencies it has. New spec
+        will have any dependencies the replacement had, and may need
+        to be normalized.
+
+        """
+        for name, dependent in self.dependents.items():
+            del dependent.dependencies[self.name]
+            dependent._add_dependency(replacement)
+
+        for name, dep in self.dependencies.items():
+            del dep.dependents[self.name]
+            del self.dependencies[dep.name]
 
 
     def _expand_virtual_packages(self):
@@ -807,18 +839,80 @@ def _expand_virtual_packages(self):
               this are infrequent, but should implement this before it is
               a problem.
         """
+        # Make an index of stuff this spec already provides
+        self_index = ProviderIndex(self.traverse(), restrict=True)
+
         changed = False
         done = False
         while not done:
             done = True
             for spec in list(self.traverse()):
-                if spack.concretizer.concretize_virtual_and_external(spec):
-                    done = False
+                replacement = None
+                if spec.virtual:
+                    replacement = self._find_provider(spec, self_index)
+                    if replacement:
+                        # TODO: may break if in-place on self but
+                        # shouldn't happen if root is traversed first.
+                        spec._replace_with(replacement)
+                        done=False
+                        break
+
+                if not replacement:
+                    # Get a list of possible replacements in order of preference.
+                    candidates = spack.concretizer.choose_virtual_or_external(spec)
+
+                    # Try the replacements in order, skipping any that cause
+                    # satisfiability problems.
+                    for replacement in candidates:
+                        if replacement is spec:
+                            break
+
+                        # Replace spec with the candidate and normalize
+                        copy = self.copy()
+                        copy[spec.name]._dup(replacement.copy(deps=False))
+
+                        try:
+                            # If there are duplicate providers or duplicate provider
+                            # deps, consolidate them and merge constraints.
+                            copy.normalize(force=True)
+                            break
+                        except SpecError as e:
+                            # On error, we'll try the next replacement.
+                            continue
+
+                # If replacement is external then trim the dependencies
+                if replacement.external:
+                    if (spec.dependencies):
+                        changed = True
+                        spec.dependencies = DependencyMap()
+                    replacement.dependencies = DependencyMap()
+
+                # TODO: could this and the stuff in _dup be cleaned up?
+                def feq(cfield, sfield):
+                    return (not cfield) or (cfield == sfield)
+
+                if replacement is spec or (feq(replacement.name, spec.name) and
+                    feq(replacement.versions, spec.versions) and
+                    feq(replacement.compiler, spec.compiler) and
+                    feq(replacement.architecture, spec.architecture) and
+                    feq(replacement.dependencies, spec.dependencies) and
+                    feq(replacement.variants, spec.variants) and
+                    feq(replacement.external, spec.external)):
+                    continue
+
+                # Refine this spec to the candidate. This uses
+                # replace_with AND dup so that it can work in
+                # place. TODO: make this more efficient.
+                if spec.virtual:
+                    spec._replace_with(replacement)
+                    changed = True
+                if spec._dup(replacement, deps=False, cleardeps=False):
                     changed = True
 
-        # If there are duplicate providers or duplicate provider deps, this
-        # consolidates them and merge constraints.
-        changed |= self.normalize(force=True)
+                self_index.update(spec)
+                done=False
+                break
+
         return changed
 
 
@@ -842,7 +936,7 @@ def concretize(self):
         force = False
 
         while changed:
-            changes = (self.normalize(force=force),
+            changes = (self.normalize(force),
                        self._expand_virtual_packages(),
                        self._concretize_helper())
             changed = any(changes)
@@ -968,8 +1062,8 @@ def _evaluate_dependency_conditions(self, name):
 
     def _find_provider(self, vdep, provider_index):
         """Find provider for a virtual spec in the provider index.
-        Raise an exception if there is a conflicting virtual
-        dependency already in this spec.
+           Raise an exception if there is a conflicting virtual
+           dependency already in this spec.
         """
         assert(vdep.virtual)
         providers = provider_index.providers_for(vdep)
@@ -1010,17 +1104,14 @@ def _merge_dependency(self, dep, visited, spec_deps, provider_index):
         """
         changed = False
 
-        # If it's a virtual dependency, try to find a provider and
-        # merge that.
+        # If it's a virtual dependency, try to find an existing
+        # provider in the spec, and merge that.
         if dep.virtual:
             visited.add(dep.name)
             provider = self._find_provider(dep, provider_index)
             if provider:
                 dep = provider
-
         else:
-            # if it's a real dependency, check whether it provides
-            # something already required in the spec.
             index = ProviderIndex([dep], restrict=True)
             for vspec in (v for v in spec_deps.values() if v.virtual):
                 if index.providers_for(vspec):
@@ -1117,13 +1208,14 @@ def normalize(self, force=False):
         # Get all the dependencies into one DependencyMap
         spec_deps = self.flat_dependencies(copy=False)
 
-        # Initialize index of virtual dependency providers
-        index = ProviderIndex(spec_deps.values(), restrict=True)
+        # Initialize index of virtual dependency providers if
+        # concretize didn't pass us one already
+        provider_index = ProviderIndex(spec_deps.values(), restrict=True)
 
         # traverse the package DAG and fill out dependencies according
         # to package files & their 'when' specs
         visited = set()
-        any_change = self._normalize_helper(visited, spec_deps, index)
+        any_change = self._normalize_helper(visited, spec_deps, provider_index)
 
         # If there are deps specified but not visited, they're not
         # actually deps of this package.  Raise an error.
@@ -1161,7 +1253,7 @@ def validate_names(self):
 
             # Ensure that variants all exist.
             for vname, variant in spec.variants.items():
-                if vname not in spec.package.variants:
+                if vname not in spec.package_class.variants:
                     raise UnknownVariantError(spec.name, vname)
 
 
@@ -1402,13 +1494,12 @@ def _dup(self, other, **kwargs):
                Whether deps should be copied too.  Set to false to copy a
                spec but not its dependencies.
         """
-
         # We don't count dependencies as changes here
         changed = True
         if hasattr(self, 'name'):
-            changed = (self.name != other.name and self.versions != other.versions and \
-                       self.architecture != other.architecture and self.compiler != other.compiler and \
-                       self.variants != other.variants and self._normal != other._normal and \
+            changed = (self.name != other.name and self.versions != other.versions and
+                       self.architecture != other.architecture and self.compiler != other.compiler and
+                       self.variants != other.variants and self._normal != other._normal and
                        self.concrete != other.concrete and self.external != other.external)
 
         # Local node attributes get copied first.

lib/spack/spack/test/__init__.py

@@ -66,7 +66,8 @@
               'database',
               'namespace_trie',
               'yaml',
-              'sbang']
+              'sbang',
+              'environment']
 
 
 def list_tests():

lib/spack/spack/test/concretize.py

@@ -24,6 +24,7 @@
 ##############################################################################
 import spack
 from spack.spec import Spec, CompilerSpec
+from spack.version import ver
 from spack.concretize import find_spec
 from spack.test.mock_packages_test import *
 
@@ -77,6 +78,14 @@ def test_concretize_variant(self):
         self.check_concretize('mpich')
 
 
+    def test_concretize_preferred_version(self):
+        spec = self.check_concretize('python')
+        self.assertEqual(spec.versions, ver('2.7.11'))
+
+        spec = self.check_concretize('python@3.5.1')
+        self.assertEqual(spec.versions, ver('3.5.1'))
+
+
     def test_concretize_with_virtual(self):
         self.check_concretize('mpileaks ^mpi')
         self.check_concretize('mpileaks ^mpi@:1.1')
@@ -142,6 +151,34 @@ def test_concretize_with_provides_when(self):
                                 for spec in spack.repo.providers_for('mpi@3')))
 
 
+    def test_concretize_two_virtuals(self):
+        """Test a package with multiple virtual dependencies."""
+        s = Spec('hypre').concretize()
+
+
+    def test_concretize_two_virtuals_with_one_bound(self):
+        """Test a package with multiple virtual dependencies and one preset."""
+        s = Spec('hypre ^openblas').concretize()
+
+
+    def test_concretize_two_virtuals_with_two_bound(self):
+        """Test a package with multiple virtual dependencies and two of them preset."""
+        s = Spec('hypre ^openblas ^netlib-lapack').concretize()
+
+
+    def test_concretize_two_virtuals_with_dual_provider(self):
+        """Test a package with multiple virtual dependencies and force a provider
+           that provides both."""
+        s = Spec('hypre ^openblas-with-lapack').concretize()
+
+
+    def test_concretize_two_virtuals_with_dual_provider_and_a_conflict(self):
+        """Test a package with multiple virtual dependencies and force a provider
+           that provides both, and another conflicting package that provides one."""
+        s = Spec('hypre ^openblas-with-lapack ^netlib-lapack')
+        self.assertRaises(spack.spec.MultipleProviderError, s.concretize)
+
+
     def test_virtual_is_fully_expanded_for_callpath(self):
         # force dependence on fake "zmpi" by asking for MPI 10.0
         spec = Spec('callpath ^mpi@10.0')
@@ -282,3 +319,9 @@ def test_find_spec_none(self):
                  Spec('e'))
         self.assertEqual(None, find_spec(s['b'], lambda s: '+foo' in s))
 
+
+    def test_compiler_child(self):
+        s = Spec('mpileaks%clang ^dyninst%gcc')
+        s.concretize()
+        self.assertTrue(s['mpileaks'].satisfies('%clang'))
+        self.assertTrue(s['dyninst'].satisfies('%gcc'))

lib/spack/spack/test/database.py

@@ -26,6 +26,7 @@
 These tests check the database is functioning properly,
 both in memory and in its file
 """
+import os.path
 import multiprocessing
 import shutil
 import tempfile

lib/spack/spack/test/environment.py

@@ -0,0 +1,73 @@
+import unittest
+import os
+from spack.environment import EnvironmentModifications
+
+
+class EnvironmentTest(unittest.TestCase):
+    def setUp(self):
+        os.environ.clear()
+        os.environ['UNSET_ME'] = 'foo'
+        os.environ['EMPTY_PATH_LIST'] = ''
+        os.environ['PATH_LIST'] = '/path/second:/path/third'
+        os.environ['REMOVE_PATH_LIST'] = '/a/b:/duplicate:/a/c:/remove/this:/a/d:/duplicate/:/f/g'
+
+    def test_set(self):
+        env = EnvironmentModifications()
+        env.set('A', 'dummy value')
+        env.set('B', 3)
+        env.apply_modifications()
+        self.assertEqual('dummy value', os.environ['A'])
+        self.assertEqual(str(3), os.environ['B'])
+
+    def test_unset(self):
+        env = EnvironmentModifications()
+        self.assertEqual('foo', os.environ['UNSET_ME'])
+        env.unset('UNSET_ME')
+        env.apply_modifications()
+        self.assertRaises(KeyError, os.environ.__getitem__, 'UNSET_ME')
+
+    def test_set_path(self):
+        env = EnvironmentModifications()
+        env.set_path('A', ['foo', 'bar', 'baz'])
+        env.apply_modifications()
+        self.assertEqual('foo:bar:baz', os.environ['A'])
+
+    def test_path_manipulation(self):
+        env = EnvironmentModifications()
+
+        env.append_path('PATH_LIST', '/path/last')
+        env.prepend_path('PATH_LIST', '/path/first')
+
+        env.append_path('EMPTY_PATH_LIST', '/path/middle')
+        env.append_path('EMPTY_PATH_LIST', '/path/last')
+        env.prepend_path('EMPTY_PATH_LIST', '/path/first')
+
+        env.append_path('NEWLY_CREATED_PATH_LIST', '/path/middle')
+        env.append_path('NEWLY_CREATED_PATH_LIST', '/path/last')
+        env.prepend_path('NEWLY_CREATED_PATH_LIST', '/path/first')
+
+        env.remove_path('REMOVE_PATH_LIST', '/remove/this')
+        env.remove_path('REMOVE_PATH_LIST', '/duplicate/')
+
+        env.apply_modifications()
+        self.assertEqual('/path/first:/path/second:/path/third:/path/last', os.environ['PATH_LIST'])
+        self.assertEqual('/path/first:/path/middle:/path/last', os.environ['EMPTY_PATH_LIST'])
+        self.assertEqual('/path/first:/path/middle:/path/last', os.environ['NEWLY_CREATED_PATH_LIST'])
+        self.assertEqual('/a/b:/a/c:/a/d:/f/g', os.environ['REMOVE_PATH_LIST'])
+
+    def test_extra_arguments(self):
+        env = EnvironmentModifications()
+        env.set('A', 'dummy value', who='Pkg1')
+        for x in env:
+            assert 'who' in x.args
+        env.apply_modifications()
+        self.assertEqual('dummy value', os.environ['A'])
+
+    def test_extend(self):
+        env = EnvironmentModifications()
+        env.set('A', 'dummy value')
+        env.set('B', 3)
+        copy_construct = EnvironmentModifications(env)
+        self.assertEqual(len(copy_construct), 2)
+        for x, y in zip(env, copy_construct):
+            assert x is y

lib/spack/spack/url.py

@@ -142,7 +142,7 @@ def split_url_extension(path):
 
 def downloaded_file_extension(path):
     """This returns the type of archive a URL refers to.  This is
-       sometimes confusing becasue of URLs like:
+       sometimes confusing because of URLs like:
 
            (1) https://github.com/petdance/ack/tarball/1.93_02
 

lib/spack/spack/util/compression.py

@@ -27,13 +27,12 @@
 from itertools import product
 from spack.util.executable import which
 
-# Supported archvie extensions.
+# Supported archive extensions.
 PRE_EXTS = ["tar"]
 EXTS     = ["gz", "bz2", "xz", "Z", "zip", "tgz"]
 
-# Add EXTS last so that .tar.gz is matched *before* tar.gz
-ALLOWED_ARCHIVE_TYPES = [".".join(l) for l in product(PRE_EXTS, EXTS)] + EXTS
-
+# Add PRE_EXTS and EXTS last so that .tar.gz is matched *before* .tar or .gz
+ALLOWED_ARCHIVE_TYPES = [".".join(l) for l in product(PRE_EXTS, EXTS)] + PRE_EXTS + EXTS
 
 def allowed_archive(path):
     return any(path.endswith(t) for t in ALLOWED_ARCHIVE_TYPES)

lib/spack/spack/util/environment.py

@@ -59,14 +59,8 @@ def path_put_first(var_name, directories):
     path_set(var_name, new_path)
 
 
-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()):
+        for key, val in sorted(os.environ.items()):
             env_file.write("%s=%s\n" % (key, val))