Merge branch 'develop' into correct-cc

lib/spack/env/cc

@@ -86,22 +86,22 @@ done
 #
 command=$(basename "$0")
 case "$command" in
-    cc|gcc|c89|c99|clang|xlc)
+    cc|c89|c99|gcc|clang|icc|pgcc|xlc)
         command="$SPACK_CC"
         language="C"
         ;;
-    c++|CC|g++|clang++|xlC)
+    c++|CC|g++|clang++|icpc|pgCC|xlc++)
         command="$SPACK_CXX"
         language="C++"
         ;;
-    f77|xlf)
-        command="$SPACK_F77"
-        language="Fortran 77"
-        ;;
-    fc|f90|f95|xlf90)
+    f90|fc|f95|gfortran|ifort|pgf90|xlf90)
         command="$SPACK_FC"
         language="Fortran 90"
         ;;
+    f77|gfortran|ifort|pgf77|xlf)
+        command="$SPACK_F77"
+        language="Fortran 77"
+        ;;
     cpp)
         mode=cpp
         ;;

lib/spack/env/clang/clang

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

lib/spack/env/clang/clang++

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

lib/spack/env/gcc/g++

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

lib/spack/env/gcc/gcc

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

lib/spack/env/gcc/gfortran

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

lib/spack/env/intel/icc

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

lib/spack/env/intel/icpc

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

lib/spack/env/intel/ifort

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

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

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

lib/spack/env/pgi/pgcc

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

lib/spack/env/pgi/pgf77

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

lib/spack/env/pgi/pgf90

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

lib/spack/env/xl/xlc

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

lib/spack/env/xl/xlc++

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

lib/spack/env/xl/xlf

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

lib/spack/env/xl/xlf90

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

lib/spack/external/pyqver2.py

@@ -30,7 +30,8 @@
 StandardModules = {
     "__future__":       (2, 1),
     "abc":              (2, 6),
-    "argparse":         (2, 7),
+# skip argparse now that it's in lib/spack/external
+#    "argparse":         (2, 7),
     "ast":              (2, 6),
     "atexit":           (2, 0),
     "bz2":              (2, 3),

lib/spack/spack/build_environment.py

@@ -88,10 +88,14 @@ def set_compiler_environment_variables(pkg):
     compiler = pkg.compiler
 
     # Set compiler variables used by CMake and autotools
-    os.environ['CC']  = join_path(spack.build_env_path, 'cc')
-    os.environ['CXX'] = join_path(spack.build_env_path, 'c++')
-    os.environ['F77'] = join_path(spack.build_env_path, 'f77')
-    os.environ['FC']  = join_path(spack.build_env_path, 'f90')
+    assert all(key in pkg.compiler.link_paths
+               for key in ('cc', 'cxx', 'f77', 'fc'))
+
+    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'])
 
     # Set SPACK compiler variables so that our wrapper knows what to call
     if compiler.cc:
@@ -110,11 +114,23 @@ def set_build_environment_variables(pkg):
     """This ensures a clean install environment when we build packages.
     """
     # Add spack build environment path with compiler wrappers first in
-    # the path.  We handle case sensitivity conflicts like "CC" and
-    # "cc" by putting one in the <build_env_path>/case-insensitive
+    # 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.
+    #
+    # 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 = [spack.build_env_path,
-                 join_path(spack.build_env_path, 'case-insensitive')]
+    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))
+
     path_put_first("PATH", env_paths)
     path_set(SPACK_ENV_PATH, env_paths)
 

lib/spack/spack/cmd/extensions.py

@@ -54,7 +54,9 @@ def extensions(parser, args):
     if not args.spec:
         tty.die("extensions requires a package spec.")
 
+    #
     # Checks
+    #
     spec = spack.cmd.parse_specs(args.spec)
     if len(spec) > 1:
         tty.die("Can only list extensions for one package.")
@@ -70,7 +72,9 @@ def extensions(parser, args):
     if not args.mode:
         args.mode = 'short'
 
+    #
     # List package names of extensions
+    #
     extensions = spack.db.extensions_for(spec)
     if not extensions:
         tty.msg("%s has no extensions." % spec.cshort_spec)
@@ -79,7 +83,9 @@ def extensions(parser, args):
     tty.msg("%d extensions:" % len(extensions))
     colify(ext.name for ext in extensions)
 
+    #
     # List specs of installed extensions.
+    #
     installed = [s.spec for s in spack.installed_db.installed_extensions_for(spec)]
     print
     if not installed:
@@ -88,7 +94,9 @@ def extensions(parser, args):
     tty.msg("%d installed:" % len(installed))
     spack.cmd.find.display_specs(installed, mode=args.mode)
 
+    #
     # List specs of activated extensions.
+    #
     activated = spack.install_layout.extension_map(spec)
     print
     if not activated:

lib/spack/spack/cmd/fetch.py

@@ -33,10 +33,13 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-n', '--no-checksum', action='store_true', dest='no_checksum',
         help="Do not check packages against checksum")
+    subparser.add_argument(
+        '-m', '--missing', action='store_true', help="Also fetch all missing dependencies")
+    subparser.add_argument(
+        '-D', '--dependencies', action='store_true', help="Also fetch all dependencies")
     subparser.add_argument(
         'packages', nargs=argparse.REMAINDER, help="specs of packages to fetch")
 
-
 def fetch(parser, args):
     if not args.packages:
         tty.die("fetch requires at least one package argument")
@@ -46,5 +49,13 @@ def fetch(parser, args):
 
     specs = spack.cmd.parse_specs(args.packages, concretize=True)
     for spec in specs:
+        if args.missing or args.dependencies:
+            to_fetch = set()
+            for s in spec.traverse():
+                package = spack.db.get(s)
+                if args.missing and package.installed:
+                    continue
+                package.do_fetch()
+
         package = spack.db.get(spec)
         package.do_fetch()

lib/spack/spack/cmd/mirror.py

@@ -54,6 +54,8 @@ def setup_parser(subparser):
         'specs', nargs=argparse.REMAINDER, help="Specs of packages to put in mirror")
     create_parser.add_argument(
         '-f', '--file', help="File with specs of packages to put in mirror.")
+    create_parser.add_argument(
+        '-D', '--dependencies', action='store_true', help="Also fetch all dependencies")
     create_parser.add_argument(
         '-o', '--one-version-per-spec', action='store_const', const=1, default=0,
         help="Only fetch one 'preferred' version per spec, not all known versions.")
@@ -118,7 +120,7 @@ def mirror_create(args):
     """Create a directory to be used as a spack mirror, and fill it with
        package archives."""
     # try to parse specs from the command line first.
-    specs = spack.cmd.parse_specs(args.specs)
+    specs = spack.cmd.parse_specs(args.specs, concretize=True)
 
     # If there is a file, parse each line as a spec and add it to the list.
     if args.file:
@@ -131,6 +133,14 @@ def mirror_create(args):
         specs = [Spec(n) for n in spack.db.all_package_names()]
         specs.sort(key=lambda s: s.format("$_$@").lower())
 
+    if args.dependencies:
+        new_specs = set()
+        for spec in specs:
+            spec.concretize()
+            for s in spec.traverse():
+                new_specs.add(s)
+        specs = list(new_specs)
+
     # Default name for directory is spack-mirror-<DATESTAMP>
     directory = args.directory
     if not directory:

lib/spack/spack/cmd/python.py

@@ -31,6 +31,8 @@
 import spack
 
 def setup_parser(subparser):
+    subparser.add_argument(
+        '-c', dest='python_command', help='Command to execute.')
     subparser.add_argument(
         'python_args', nargs=argparse.REMAINDER, help="File to run plus arguments.")
 
@@ -38,7 +40,8 @@ def setup_parser(subparser):
 
 def python(parser, args):
     # Fake a main python shell by setting __name__ to __main__.
-    console = code.InteractiveConsole({'__name__' : '__main__'})
+    console = code.InteractiveConsole({'__name__' : '__main__',
+                                       'spack'    : spack})
 
     if "PYTHONSTARTUP" in os.environ:
         startup_file = os.environ["PYTHONSTARTUP"]
@@ -47,7 +50,10 @@ def python(parser, args):
                 console.runsource(startup.read(), startup_file, 'exec')
 
     python_args = args.python_args
-    if python_args:
+    python_command = args.python_command
+    if python_command:
+        console.runsource(python_command)
+    elif python_args:
         sys.argv = python_args
         with open(python_args[0]) as file:
             console.runsource(file.read(), python_args[0], 'exec')

lib/spack/spack/cmd/uninstall.py

@@ -42,9 +42,9 @@ def setup_parser(subparser):
         help="Remove regardless of whether other packages depend on this one.")
     subparser.add_argument(
         '-a', '--all', action='store_true', dest='all',
-        help="USE CAREFULLY.  Remove ALL installed packages that match each supplied spec. " +
-        "i.e., if you say uninstall libelf, ALL versions of libelf are uninstalled. " +
-        "This is both useful and dangerous, like rm -r.")
+        help="USE CAREFULLY. Remove ALL installed packages that match each " +
+        "supplied spec. i.e., if you say uninstall libelf, ALL versions of " +
+        "libelf are uninstalled. This is both useful and dangerous, like rm -r.")
     subparser.add_argument(
         'packages', nargs=argparse.REMAINDER, help="specs of packages to uninstall")
 
@@ -81,7 +81,8 @@ def uninstall(parser, args):
                     pkgs.append(s.package)
 
                 except spack.packages.UnknownPackageError, e:
-                    # The package.py file has gone away -- but still want to uninstall.
+                    # The package.py file has gone away -- but still want to
+                    # uninstall.
                     spack.Package(s).do_uninstall(force=True)
 
         # Sort packages to be uninstalled by the number of installed dependents

lib/spack/spack/compilers/clang.py

@@ -37,6 +37,12 @@ class Clang(Compiler):
     # Subclasses use possible names of Fortran 90 compiler
     fc_names = []
 
+    # Named wrapper links within spack.build_env_path
+    link_paths = { 'cc'  : 'clang/clang',
+                   'cxx' : 'clang/clang++',
+                   # Use default wrappers for fortran, in case provided in compilers.yaml
+                   'f77' : 'f77',
+                   'fc'  : 'f90' }
 
     @classmethod
     def default_version(self, comp):

lib/spack/spack/compilers/gcc.py

@@ -42,6 +42,12 @@ class Gcc(Compiler):
     # MacPorts builds gcc versions with prefixes and -mp-X.Y suffixes.
     suffixes = [r'-mp-\d\.\d']
 
+    # Named wrapper links within spack.build_env_path
+    link_paths = {'cc'  : 'gcc/gcc',
+                  'cxx' : 'gcc/g++',
+                  'f77' : 'gcc/gfortran',
+                  'fc'  : 'gcc/gfortran' }
+
     @property
     def cxx11_flag(self):
         if self.version < ver('4.3'):

lib/spack/spack/compilers/intel.py

@@ -37,6 +37,12 @@ class Intel(Compiler):
     # Subclasses use possible names of Fortran 90 compiler
     fc_names = ['ifort']
 
+    # Named wrapper links within spack.build_env_path
+    link_paths = { 'cc'  : 'intel/icc',
+                   'cxx' : 'intel/icpc',
+                   'f77' : 'intel/ifort',
+                   'fc'  : 'intel/ifort' }
+
     @property
     def cxx11_flag(self):
         if self.version < ver('11.1'):

lib/spack/spack/compilers/pgi.py

@@ -37,6 +37,12 @@ class Pgi(Compiler):
     # Subclasses use possible names of Fortran 90 compiler
     fc_names = ['pgf95', 'pgf90']
 
+    # Named wrapper links within spack.build_env_path
+    link_paths = { 'cc'  : 'pgi/pgcc',
+                   'cxx' : 'pgi/case-insensitive/pgCC',
+                   'f77' : 'pgi/pgf77',
+                   'fc'  : 'pgi/pgf90' }
+
     @classmethod
     def default_version(cls, comp):
         """The '-V' option works for all the PGI compilers.

lib/spack/spack/compilers/xl.py

@@ -38,6 +38,12 @@ class Xl(Compiler):
     # Subclasses use possible names of Fortran 90 compiler
     fc_names = ['xlf90','xlf90_r','xlf95','xlf95_r','xlf2003','xlf2003_r','xlf2008','xlf2008_r']
 
+    # Named wrapper links within spack.build_env_path
+    link_paths = { 'cc'  : 'xl/xlc',
+                   'cxx' : 'xl/xlc++',
+                   'f77' : 'xl/xlf',
+                   'fc'  : 'xl/xlf90' }
+
     @property
     def cxx11_flag(self):
         if self.version < ver('13.1'):

lib/spack/spack/database.py

@@ -54,6 +54,7 @@
 from spack.version import Version
 from spack.spec import Spec
 from spack.error import SpackError
+from spack.packages import UnknownPackageError
 
 # DB goes in this directory underneath the root
 _db_dirname = '.spack-db'

lib/spack/spack/hooks/extensions.py

@@ -27,9 +27,7 @@
 
 
 def pre_uninstall(pkg):
-    # Need to do this b/c uninstall does not automatically do it.
-    # TODO: store full graph info in stored .spec file.
-    pkg.spec.normalize()
+    assert(pkg.spec.concrete)
 
     if pkg.is_extension:
         if pkg.activated:

lib/spack/spack/mirror.py

@@ -146,7 +146,7 @@ def create(path, specs, **kwargs):
         stage = None
         try:
             # create a subdirectory for the current package@version
-            archive_path = os.path.abspath(join_path(path, mirror_archive_path(spec)))
+            archive_path = os.path.abspath(join_path(mirror_root, mirror_archive_path(spec)))
             subdir = os.path.dirname(archive_path)
             mkdirp(subdir)
 

lib/spack/spack/package.py

@@ -487,9 +487,15 @@ def extendee_spec(self):
             if name == dep.name:
                 return dep
 
-        # Otherwise return the spec from the extends() directive
-        spec, kwargs = self.extendees[name]
-        return spec
+        # if the spec is concrete already, then it extends something
+        # that is an *optional* dependency, and the dep isn't there.
+        if self.spec._concrete:
+            return None
+        else:
+            # If it's not concrete, then return the spec from the
+            # extends() directive since that is all we know so far.
+            spec, kwargs = self.extendees[name]
+            return spec
 
 
     @property
@@ -497,18 +503,28 @@ def extendee_args(self):
         """Spec of the extendee of this package, or None if it is not an extension."""
         if not self.extendees:
             return None
+
+        # TODO: allow multiple extendees.
         name = next(iter(self.extendees))
         return self.extendees[name][1]
 
 
     @property
     def is_extension(self):
-        return len(self.extendees) > 0
+        # if it is concrete, it's only an extension if it actually
+        # dependes on the extendee.
+        if self.spec._concrete:
+            return self.extendee_spec is not None
+        else:
+            # If not, then it's an extension if it *could* be an extension
+            return bool(self.extendees)
 
 
     def extends(self, spec):
-        return (spec.name in self.extendees and
-                spec.satisfies(self.extendees[spec.name][0]))
+        if not spec.name in self.extendees:
+            return False
+        s = self.extendee_spec
+        return s and s.satisfies(spec)
 
 
     @property

lib/spack/spack/test/python_version.py

@@ -63,10 +63,6 @@ def check_python_versions(self, *files):
         all_issues = {}
 
         for fn in files:
-            if fn != '/Users/gamblin2/src/spack/var/spack/packages/vim/package.py':
-                continue
-            print fn
-
             with open(fn) as pyfile:
                 versions = pyqver2.get_versions(pyfile.read())
                 for ver, reasons in versions.items():