Merge remote-tracking branch 'upstream/develop' into develop

lib/spack/spack/hooks/sbang.py

@@ -35,7 +35,7 @@
 shebang_limit = 127
 
 def shebang_too_long(path):
-    """Detects whether an file has a shebang line that is too long."""
+    """Detects whether a file has a shebang line that is too long."""
     with open(path, 'r') as script:
         bytes = script.read(2)
         if bytes != '#!':
@@ -47,14 +47,21 @@ def shebang_too_long(path):
 
 def filter_shebang(path):
     """Adds a second shebang line, using sbang, at the beginning of a file."""
+    with open(path, 'r') as original_file:
+        original = original_file.read()
+
+    # This line will be prepended to file
+    new_sbang_line = '#!/bin/bash %s/bin/sbang\n' % spack.spack_root
+
+    # Skip files that are already using sbang.
+    if original.startswith(new_sbang_line):
+        return
+
     backup = path + ".shebang.bak"
     os.rename(path, backup)
 
-    with open(backup, 'r') as bak_file:
-        original = bak_file.read()
-
     with open(path, 'w') as new_file:
-        new_file.write('#!/bin/bash %s/bin/sbang\n' % spack.spack_root)
+        new_file.write(new_sbang_line)
         new_file.write(original)
 
     copy_mode(backup, path)
@@ -63,15 +70,29 @@ def filter_shebang(path):
     tty.warn("Patched overly long shebang in %s" % path)
 
 
+def filter_shebangs_in_directory(directory):
+    for file in os.listdir(directory):
+        path = os.path.join(directory, file)
+
+        # only handle files
+        if not os.path.isfile(path):
+            continue
+
+        # only handle links that resolve within THIS package's prefix.
+        if os.path.islink(path):
+            real_path = os.path.realpath(path)
+            if not real_path.startswith(directory + os.sep):
+                continue
+
+        # test the file for a long shebang, and filter
+        if shebang_too_long(path):
+            filter_shebang(path)
+
+
 def post_install(pkg):
     """This hook edits scripts so that they call /bin/bash
        $spack_prefix/bin/sbang instead of something longer than the
        shebang limit."""
     if not os.path.isdir(pkg.prefix.bin):
         return
-
+    filter_shebangs_in_directory(pkg.prefix.bin)
-    for file in os.listdir(pkg.prefix.bin):
-        path = os.path.join(pkg.prefix.bin, file)
-        if shebang_too_long(path):
-            filter_shebang(path)
-

lib/spack/spack/package.py

@@ -825,7 +825,7 @@ def _resource_stage(self, resource):
 
 
     def do_install(self,
-                   keep_prefix=False,  keep_stage=None, ignore_deps=False,
+                   keep_prefix=False,  keep_stage=False, ignore_deps=False,
                    skip_patch=False, verbose=False, make_jobs=None, fake=False):
         """Called by commands to install a package and its dependencies.
 
@@ -834,8 +834,9 @@ def do_install(self,
 
         Args:
         keep_prefix -- Keep install prefix on failure. By default, destroys it.
-        keep_stage  -- Set to True or false to always keep or always delete stage.
+        keep_stage  -- By default, stage is destroyed only if there are no
-                       By default, stage is destroyed only if there are no exceptions.
+                       exceptions during build. Set to True to keep the stage
+                       even with exceptions.
         ignore_deps -- Do not install dependencies before installing this package.
         fake        -- Don't really build -- install fake stub files instead.
         skip_patch  -- Skip patch stage of build if True.

lib/spack/spack/stage.py

@@ -88,7 +88,8 @@ class Stage(object):
     similar, and are intended to persist for only one run of spack.
     """
 
-    def __init__(self, url_or_fetch_strategy, name=None, mirror_path=None, keep=None):
+    def __init__(self, url_or_fetch_strategy,
+                 name=None, mirror_path=None, keep=False):
         """Create a stage object.
            Parameters:
              url_or_fetch_strategy
@@ -108,10 +109,9 @@ def __init__(self, url_or_fetch_strategy, name=None, mirror_path=None, keep=None
 
              keep
                  By default, when used as a context manager, the Stage
-                 is cleaned up when everything goes well, and it is
+                 is deleted on exit when no exceptions are raised.
-                 kept intact when an exception is raised. You can
+                 Pass True to keep the stage intact even if no
-                 override this behavior by setting keep to True
+                 exceptions are raised.
-                 (always keep) or False (always delete).
         """
         # TODO: fetch/stage coupling needs to be reworked -- the logic
         # TODO: here is convoluted and not modular enough.
@@ -166,12 +166,8 @@ def __exit__(self, exc_type, exc_val, exc_tb):
         Returns:
             Boolean
         """
-        if self.keep is None:
+        # Delete when there are no exceptions, unless asked to keep.
-            # Default: delete when there are no exceptions.
+        if exc_type is None and not self.keep:
-            if exc_type is None: self.destroy()
-
-        elif not self.keep:
-            # Overridden. Either always keep or always delete.
             self.destroy()
 
 
@@ -195,8 +191,8 @@ def _need_to_create_path(self):
             real_tmp = os.path.realpath(self.tmp_root)
 
             if spack.use_tmp_stage:
-                # If we're using a tmp dir, it's a link, and it points at the right spot,
+                # If we're using a tmp dir, it's a link, and it points at the
-                # then keep it.
+                # right spot, then keep it.
                 if (real_path.startswith(real_tmp) and os.path.exists(real_path)):
                     return False
                 else:
@@ -441,7 +437,7 @@ def __enter__(self):
 
     def __exit__(self, exc_type, exc_val, exc_tb):
         for item in reversed(self):
-            item.keep = getattr(self, 'keep', None)
+            item.keep = getattr(self, 'keep', False)
             item.__exit__(exc_type, exc_val, exc_tb)
 
     #

lib/spack/spack/test/__init__.py

@@ -65,7 +65,8 @@
               'lock',
               'database',
               'namespace_trie',
-              'yaml']
+              'yaml',
+              'sbang']
 
 
 def list_tests():

lib/spack/spack/test/sbang.py

@@ -0,0 +1,93 @@
+##############################################################################
+# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+"""\
+Test that Spack's shebang filtering works correctly.
+"""
+import os
+import unittest
+import tempfile
+import shutil
+
+from llnl.util.filesystem import *
+from spack.hooks.sbang import filter_shebangs_in_directory
+import spack
+
+short_line = "#!/this/is/short/bin/bash\n"
+long_line  = "#!/this/" + ('x' * 200) + "/is/long\n"
+sbang_line = '#!/bin/bash %s/bin/sbang\n' % spack.spack_root
+last_line = "last!\n"
+
+class SbangTest(unittest.TestCase):
+    def setUp(self):
+        self.tempdir = tempfile.mkdtemp()
+
+        # make sure we can ignore non-files
+        directory = os.path.join(self.tempdir, 'dir')
+        mkdirp(directory)
+
+        # Script with short shebang
+        self.short_shebang = os.path.join(self.tempdir, 'short')
+        with open(self.short_shebang, 'w') as f:
+            f.write(short_line)
+            f.write(last_line)
+
+        # Script with long shebang
+        self.long_shebang = os.path.join(self.tempdir, 'long')
+        with open(self.long_shebang, 'w') as f:
+            f.write(long_line)
+            f.write(last_line)
+
+        # Script already using sbang.
+        self.has_shebang = os.path.join(self.tempdir, 'shebang')
+        with open(self.has_shebang, 'w') as f:
+            f.write(sbang_line)
+            f.write(long_line)
+            f.write(last_line)
+
+
+    def tearDown(self):
+         shutil.rmtree(self.tempdir, ignore_errors=True)
+
+
+
+    def test_shebang_handling(self):
+        filter_shebangs_in_directory(self.tempdir)
+
+        # Make sure this is untouched
+        with open(self.short_shebang, 'r') as f:
+            self.assertEqual(f.readline(), short_line)
+            self.assertEqual(f.readline(), last_line)
+
+        # Make sure this got patched.
+        with open(self.long_shebang, 'r') as f:
+            self.assertEqual(f.readline(), sbang_line)
+            self.assertEqual(f.readline(), long_line)
+            self.assertEqual(f.readline(), last_line)
+
+        # Make sure this is untouched
+        with open(self.has_shebang, 'r') as f:
+            self.assertEqual(f.readline(), sbang_line)
+            self.assertEqual(f.readline(), long_line)
+            self.assertEqual(f.readline(), last_line)

lib/spack/spack/test/stage.py

@@ -277,3 +277,38 @@ def test_restage(self):
             self.check_chdir_to_source(stage, stage_name)
             self.assertFalse('foobar' in os.listdir(stage.source_path))
         self.check_destroy(stage, stage_name)
+
+
+    def test_no_keep_without_exceptions(self):
+        with Stage(archive_url, name=stage_name, keep=False) as stage:
+            pass
+        self.check_destroy(stage, stage_name)
+
+
+    def test_keep_without_exceptions(self):
+        with Stage(archive_url, name=stage_name, keep=True) as stage:
+            pass
+        path = self.get_stage_path(stage, stage_name)
+        self.assertTrue(os.path.isdir(path))
+
+
+    def test_no_keep_with_exceptions(self):
+        try:
+            with Stage(archive_url, name=stage_name, keep=False) as stage:
+                raise Exception()
+
+            path = self.get_stage_path(stage, stage_name)
+            self.assertTrue(os.path.isdir(path))
+        except:
+            pass # ignore here.
+
+
+    def test_keep_exceptions(self):
+        try:
+            with Stage(archive_url, name=stage_name, keep=True) as stage:
+                raise Exception()
+
+            path = self.get_stage_path(stage, stage_name)
+            self.assertTrue(os.path.isdir(path))
+        except:
+            pass # ignore here.

var/spack/repos/builtin/packages/hdf5/package.py

@@ -46,7 +46,6 @@ class Hdf5(Package):
 
     variant('cxx', default=True, description='Enable C++ support')
     variant('fortran', default=True, description='Enable Fortran support')
-    variant('unsupported', default=True, description='Enables unsupported configuration options')
 
     variant('mpi', default=False, description='Enable MPI support')
     variant('szip', default=False, description='Enable szip support')
@@ -74,6 +73,13 @@ def install(self, spec, prefix):
         self.validate(spec)
         # Handle compilation after spec validation
         extra_args = []
+
+        # Always enable this option. This does not actually enable any
+        # features: it only *allows* the user to specify certain
+        # combinations of other arguments. Enabling it just skips a
+        # sanity check in configure, so this doesn't merit a variant.
+        extra_args.append("--enable-unsupported")
+
         if '+debug' in spec:
             extra_args.append('--enable-debug=all')
         else:
@@ -84,9 +90,6 @@ def install(self, spec, prefix):
         else:
             extra_args.append('--enable-static-exec')
 
-        if '+unsupported' in spec:
-            extra_args.append("--enable-unsupported")
-
         if '+cxx' in spec:
             extra_args.append('--enable-cxx')
 

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

@@ -28,8 +28,9 @@ class Mpfr(Package):
     """The MPFR library is a C library for multiple-precision
        floating-point computations with correct rounding."""
     homepage = "http://www.mpfr.org"
-    url      = "http://www.mpfr.org/mpfr-current/mpfr-3.1.3.tar.bz2"
+    url      = "https://gforge.inria.fr/frs/download.php/latestfile/159/mpfr-3.1.2.tar.bz2"
 
+    version('3.1.4', 'b8a2f6b0e68bef46e53da2ac439e1cf4')
     version('3.1.3', '5fdfa3cfa5c86514ee4a241a1affa138')
     version('3.1.2', 'ee2c3ac63bf0c2359bf08fc3ee094c19')
 

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

@@ -15,6 +15,7 @@ class Petsc(Package):
     version('3.5.3', 'd4fd2734661e89f18ac6014b5dd1ef2f')
     version('3.5.2', 'ad170802b3b058b5deb9cd1f968e7e13')
     version('3.5.1', 'a557e029711ebf425544e117ffa44d8f')
+    version('3.4.4', '7edbc68aa6d8d6a3295dd5f6c2f6979d')
 
     variant('shared', default=True, description='Enables the build of shared libraries')
     variant('mpi', default=True, description='Activates MPI support')
@@ -25,21 +26,21 @@ class Petsc(Package):
     variant('boost', default=True, description='Activates support for Boost')
     variant('hypre', default=True, description='Activates support for Hypre')
 
-    # Build dependencies
-    depends_on('python @2.6:2.9')  # requires Python for building
-
     # Virtual dependencies
     depends_on('blas')
     depends_on('lapack')
     depends_on('mpi', when='+mpi')
 
+    # Build dependencies
+    depends_on('python @2.6:2.7')
+
     # Other dependencies
     depends_on('boost', when='+boost')
     depends_on('metis', when='+metis')
 
-    depends_on('hdf5~cxx~unsupported+mpi', when='+hdf5+mpi')
+    depends_on('hdf5+mpi', when='+hdf5+mpi')
     depends_on('parmetis', when='+metis+mpi')
-    depends_on('hypre', when='+hypre+mpi')
+    depends_on('hypre',    when='+hypre+mpi')
 
     def mpi_dependent_options(self):
         if '~mpi' in self.spec:
@@ -50,7 +51,12 @@ def mpi_dependent_options(self):
                 '--with-mpi=0'
             ]
             error_message_fmt = '\t{library} support requires "+mpi" to be activated'
-            errors = [error_message_fmt.format(library=x) for x in ('hdf5', 'hypre') if ('+'+x) in self.spec]
+
+            # If mpi is disabled (~mpi), it's an error to have any of these enabled.
+            # This generates a list of any such errors.
+            errors = [error_message_fmt.format(library=x)
+                      for x in ('hdf5', 'hypre', 'parmetis')
+                      if ('+'+x) in self.spec]
             if errors:
                 errors = ['incompatible variants given'] + errors
                 raise RuntimeError('\n'.join(errors))
@@ -70,7 +76,7 @@ def install(self, spec, prefix):
             '--with-blas-lapack-dir=%s' % spec['lapack'].prefix
         ])
         # Activates library support if needed
-        for library in ('metis', 'boost', 'hfd5', 'hypre', 'parmetis'):
+        for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis'):
             options.append(
                 '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0'))
             )
@@ -79,8 +85,8 @@ def install(self, spec, prefix):
                     '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix)
                 )
 
-
         configure('--prefix=%s' % prefix, *options)
+
         # PETSc has its own way of doing parallel make.
         make('MAKE_NP=%s' % make_jobs, parallel=False)
         make("install")

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

@@ -12,33 +12,44 @@ class Thrift(Package):
 
     version('0.9.2', '89f63cc4d0100912f4a1f8a9dee63678')
 
-    extends("python")
+    # Currently only support for c-family and python
+    variant('c', default=True, description="Build support for C-family languages")
+    variant('python', default=True, description="Build support for python")
 
-    depends_on("autoconf")
+    depends_on('jdk')
-    depends_on("automake")
+    depends_on('autoconf')
-    depends_on("bison")
+    depends_on('automake')
-    depends_on("boost")
+    depends_on('libtool')
-    depends_on("flex")
+    depends_on('boost@1.53:')
-    depends_on("jdk")
+    depends_on('bison')
-    depends_on("libtool")
+    depends_on('flex')
-    depends_on("openssl")
+    depends_on('openssl')
-    depends_on("python")
+
+    # Variant dependencies
+    extends('python', when='+python')
+
+    depends_on('zlib', when='+c')
+    depends_on('libevent', when='+c')
 
-    # Compilation fails for most languages, fortunately cpp installs fine
-    # All other languages (yes, including C) are omitted until someone needs them
     def install(self, spec, prefix):
-        env["PY_PREFIX"]   = prefix
+        env['PY_PREFIX'] = prefix
-        env["JAVA_PREFIX"] = prefix
+        env['JAVA_HOME'] = spec['jdk'].prefix
 
-        configure("--prefix=%s" % prefix,
+        # configure options
-                  "--with-boost=%s" % spec['boost'].prefix,
+        options = ['--prefix=%s' % prefix]
-                  "--with-c=no",
+
-                  "--with-go=no",
+        options.append('--with-boost=%s' % spec['boost'].prefix)
-                  "--with-python=yes",
+        options.append('--enable-tests=no')
-                  "--with-lua=no",
+
-                  "--with-php=no",
+        options.append('--with-c=%s' % ('yes' if '+c' in spec else 'no'))
-                  "--with-qt4=no",
+        options.append('--with-python=%s' % ('yes' if '+python' in spec else 'no'))
-                  "--enable-tests=no")
+        options.append('--with-java=%s' % ('yes' if '+java' in spec else 'no'))
+        options.append('--with-go=%s' % ('yes' if '+go' in spec else 'no'))
+        options.append('--with-lua=%s' % ('yes' if '+lua' in spec else 'no'))
+        options.append('--with-php=%s' % ('yes' if '+php' in spec else 'no'))
+        options.append('--with-qt4=%s' % ('yes' if '+qt4' in spec else 'no'))
+
+        configure(*options)
 
         make()
         make("install")