Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases

Conflicts:
	var/spack/repos/builtin/packages/swiftsim/package.py

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

@@ -0,0 +1,53 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Gts(Package):
+    """GTS stands for the GNU Triangulated Surface Library.
+
+    It is an Open Source Free Software Library intended to provide a set of
+    useful functions to deal with 3D surfaces meshed with interconnected
+    triangles. The source code is available free of charge under the Free
+    Software LGPL license.
+
+    The code is written entirely in C with an object-oriented approach
+    based mostly on the design of GTK+. Careful attention is paid to
+    performance related issues as the initial goal of GTS is to provide a
+    simple and efficient library to scientists dealing with 3D computational
+    surface meshes.
+    """
+
+    homepage = "http://gts.sourceforge.net/index.html"
+    url = "http://gts.sourceforge.net/tarballs/gts-snapshot-121130.tar.gz"
+
+    version('121130', '023ebb6b13b8707534182a3ef0d12908')
+
+    depends_on('glib')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+        make()
+        make('install')

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

@@ -0,0 +1,76 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Hmmer(Package):
+    """HMMER is used for searching sequence databases for sequence homologs,
+    and for making sequence alignments. It implements methods using
+    probabilistic models called profile hidden Markov models (profile HMMs).
+    """
+    homepage = 'http://www.hmmer.org'
+    url      = 'http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz'
+
+    version('3.1b2', 'c8c141018bc0ccd7fc37b33f2b945d5f')
+    version('3.0',   '4cf685f3bc524ba5b5cdaaa070a83588')
+    version('2.4i',  'dab234c87e026ac1de942450750acd20')
+    version('2.3.2', '5f073340c0cf761288f961a73821228a')
+    version('2.3.1', 'c724413e5761c630892506698a4716e2')
+
+    variant('mpi', default=True,  description='Compile with MPI')
+    variant('gsl', default=False, description='Compile with GSL')
+
+    depends_on('mpi', when='+mpi')
+    depends_on('gsl', when='+gsl')
+
+    def url_for_version(self, version):
+        base_url = 'http://eddylab.org/software'
+
+        if version >= Version('3.0'):
+            return '{0}/hmmer3/{1}/hmmer-{1}.tar.gz'.format(base_url, version)
+        else:
+            return '{0}/hmmer/{1}/hmmer-{1}.tar.gz'.format(base_url, version)
+
+    def install(self, spec, prefix):
+        configure_args = [
+            '--prefix={0}'.format(prefix)
+        ]
+
+        if '+gsl' in self.spec:
+            configure_args.extend([
+                '--with-gsl',
+                'LIBS=-lgsl -lgslcblas'
+            ])
+
+        if '+mpi' in self.spec:
+            configure_args.append('--enable-mpi')
+
+        configure(*configure_args)
+        make()
+
+        if self.run_tests:
+            make('check')
+
+        make('install')

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

@@ -63,6 +63,7 @@ class Openmpi(Package):
     list_url = "http://www.open-mpi.org/software/ompi/"
     list_depth = 3
 
+    version('2.0.0', 'cdacc800cb4ce690c1f1273cb6366674')
     version('1.10.3', 'e2fe4513200e2aaa1500b762342c674b')
     version('1.10.2', 'b2f43d9635d2d52826e5ef9feb97fd4c')
     version('1.10.1', 'f0fcd77ed345b7eafb431968124ba16e')
@@ -101,6 +102,7 @@ class Openmpi(Package):
 
     provides('mpi@:2.2', when='@1.6.5')
     provides('mpi@:3.0', when='@1.7.5:')
+    provides('mpi@:3.1', when='@2.0.0:')
 
     depends_on('hwloc')
     depends_on('sqlite', when='+sqlite3')
@@ -169,7 +171,8 @@ def install(self, spec, prefix):
             '--with-psm2' if '+psm2' in spec else '--without-psm2',
             '--with-mxm' if '+mxm' in spec else '--without-mxm',
             # Other options
-            '--enable-mpi-thread-multiple' if '+thread_multiple' in spec else '--disable-mpi-thread-multiple',  # NOQA: ignore=E501
+            ('--enable-mpi-thread-multiple' if '+thread_multiple' in spec
+                else '--disable-mpi-thread-multiple'),
             '--with-pmi' if '+pmi' in spec else '--without-pmi',
             '--with-sqlite3' if '+sqlite3' in spec else '--without-sqlite3',
             '--enable-vt' if '+vt' in spec else '--disable-vt'

var/spack/repos/builtin/packages/py-numpy/package.py

@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyNumpy(Package):
     """NumPy is the fundamental package for scientific computing with Python.
     It contains among other things: a powerful N-dimensional array object,
@@ -38,7 +39,6 @@ class PyNumpy(Package):
     version('1.9.2',  'a1ed53432dbcd256398898d35bc8e645')
     version('1.9.1',  '78842b73560ec378142665e712ae4ad9')
 
-
     variant('blas',   default=True)
     variant('lapack', default=True)
 
@@ -63,6 +63,6 @@ def install(self, spec, prefix):
                 f.write('[DEFAULT]\n')
                 f.write('libraries=%s\n'    % ','.join(libraries))
                 f.write('library_dirs=%s\n' % ':'.join(library_dirs))
+                f.write('rpath=%s\n' % ':'.join(library_dirs))
 
         python('setup.py', 'install', '--prefix=%s' % prefix)
-

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

@@ -38,16 +38,29 @@ class Python(Package):
     homepage = "http://www.python.org"
     url      = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz"
 
+    version('3.5.2', '3fe8434643a78630c61c6464fe2e7e72')
     version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe')
     version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36')
-    version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True)
+    version('3.4.3', '4281ff86778db65892c05151d5de738d')
+    version('3.3.6', 'cdb3cd08f96f074b3f3994ccb51063e9')
+    version('3.2.6', '23815d82ae706e9b781ca65865353d39')
+    version('3.1.5', '02196d3fc7bc76bdda68aa36b0dd16ab')
+    version('2.7.12', '88d61f82e3616a4be952828b3694109d', preferred=True)
+    version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b')
     version('2.7.10', 'd7547558fd673bd9d38e2108c6b42521')
     version('2.7.9', '5eebcaa0030dc4061156d3429657fb83')
     version('2.7.8', 'd4bca0159acb0b44a781292b5231936f')
 
     extendable = True
 
-    variant('ucs4', default=False, description='Enable UCS4 unicode strings')
+    variant('ucs4', default=False, description='Enable UCS4 (wide) unicode strings')
+    # From https://docs.python.org/2/c-api/unicode.html: Python's default
+    # builds use a 16-bit type for Py_UNICODE and store Unicode values
+    # internally as UCS2. It is also possible to build a UCS4 version of Python
+    # (most recent Linux distributions come with UCS4 builds of Python).  These
+    # builds then use a 32-bit type for Py_UNICODE and store Unicode data
+    # internally as UCS4. Note that UCS2 and UCS4 Python builds are not binary
+    # compatible.
 
     depends_on("openssl")
     depends_on("bzip2")
@@ -85,7 +98,13 @@ def install(self, spec, prefix):
         ]
 
         if '+ucs4' in spec:
-            config_args.append('--enable-unicode=ucs4')
+            if spec.satisfies('@:2.7'):
+                config_args.append('--enable-unicode=ucs4')
+            elif spec.satisfies('@3.0:3.2'):
+                config_args.append('--with-wide-unicode')
+            elif spec.satisfies('@3.3:'):
+                # https://docs.python.org/3.3/whatsnew/3.3.html
+                raise ValueError('+ucs4 variant not compatible with Python 3.3 and beyond')  # NOQA: ignore=E501
 
         if spec.satisfies('@3:'):
             config_args.append('--without-ensurepip')

var/spack/repos/builtin/packages/r-ggvis/package.py

@@ -0,0 +1,51 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RGgvis(Package):
+    """An implementation of an interactive grammar of graphics, taking the best
+    parts of 'ggplot2', combining them with the reactive framework from 'shiny'
+    and web graphics from 'vega'."""
+
+    homepage = "http://ggvis.rstudio.com/"
+    url      = "https://cran.r-project.org/src/contrib/ggvis_0.4.2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/ggvis"
+
+    version('0.4.2', '039f45e5c7f1e0652779163d7d99f922')
+
+    extends('R')
+
+    depends_on('r-assertthat')
+    depends_on('r-jsonlite')
+    depends_on('r-shiny')
+    depends_on('r-magrittr')
+    depends_on('r-dplyr')
+    depends_on('r-lazyeval')
+    depends_on('r-htmltools')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-htmltools/package.py

@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RHtmltools(Package):
+    """Tools for HTML generation and output."""
+
+    homepage = "https://github.com/rstudio/htmltools"
+    url      = "https://cran.r-project.org/src/contrib/htmltools_0.3.5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/htmltools"
+
+    version('0.3.5', '5f001aff4a39e329f7342dcec5139724')
+
+    extends('R')
+
+    depends_on('r-digest')
+    depends_on('r-rcpp')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-httpuv/package.py

@@ -0,0 +1,49 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RHttpuv(Package):
+    """Provides low-level socket and protocol support for handling HTTP and
+    WebSocket requests directly from within R. It is primarily intended as a
+    building block for other packages, rather than making it particularly easy
+    to create complete web applications using httpuv alone. httpuv is built on
+    top of the libuv and http-parser C libraries, both of which were developed
+    by Joyent, Inc. (See LICENSE file for libuv and http-parser license
+    information.)"""
+
+    homepage = "https://github.com/rstudio/httpuv"
+    url      = "https://cran.r-project.org/src/contrib/httpuv_1.3.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/httpuv"
+
+    version('1.3.3', 'c78ae068cf59e949b9791be987bb4489')
+
+    extends('R')
+
+    depends_on('r-rcpp')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-shiny/package.py

@@ -0,0 +1,52 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RShiny(Package):
+    """Makes it incredibly easy to build interactive web applications with R.
+    Automatic "reactive" binding between inputs and outputs and extensive
+    pre-built widgets make it possible to build beautiful, responsive, and
+    powerful applications with minimal effort."""
+
+    homepage = "http://shiny.rstudio.com/"
+    url      = "https://cran.r-project.org/src/contrib/shiny_0.13.2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/shiny"
+
+    version('0.13.2', 'cb5bff7a28ad59ec2883cd0912ca9611')
+
+    extends('R')
+
+    depends_on('r-httpuv')
+    depends_on('r-mime')
+    depends_on('r-jsonlite')
+    depends_on('r-xtable')
+    depends_on('r-digest')
+    depends_on('r-htmltools')
+    depends_on('r-R6')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-xtable/package.py

@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RXtable(Package):
+    """Coerce data to LaTeX and HTML tables."""
+
+    homepage = "http://xtable.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/xtable_1.8-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/xtable"
+
+    version('1.8-2', '239e4825cd046156a67efae3aac01d86')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)