Merge remote branch 'origin/develop' into develop

2017-05-18 13:47:50 -05:00 · 2017-05-18 13:47:50 -05:00 · fcd3b90326
commit fcd3b90326
parent 13508a2e6b 04ccb8f774
11 changed files with 343 additions and 2 deletions
--- a/var/spack/repos/builtin/packages/gnupg/package.py
+++ b/var/spack/repos/builtin/packages/gnupg/package.py
@ -0,0 +1,50 @@
+##############################################################################
+# 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 Gnupg(AutotoolsPackage):
+    """GnuPG is a complete and free implementation of the OpenPGP
+       standard as defined by RFC4880 """
+
+    homepage = "https://gnupg.org/index.html"
+    url = "https://gnupg.org/ftp/gcrypt/gnupg/gnupg-2.1.21.tar.bz2"
+
+    version('2.1.21', '685ebf4c3a7134ba0209c96b18b2f064')
+
+    depends_on('libgcrypt')
+    depends_on('libassuan')
+    depends_on('libksba')
+    depends_on('libgpg-error')
+    depends_on('npth')
+
+    def configure_args(self):
+        args = ['--with-npth-prefix=%s' % self.spec['npth'].prefix,
+                '--with-libgcrypt-prefix=%s' % self.spec['libgcrypt'].prefix,
+                '--with-libksba-prefixx=%s' % self.spec['libksba'].prefix,
+                '--with-libassuan-prefix=%s' % self.spec['libassuan'].prefix,
+                '--with-libpgp-error-prefix=%s' %
+                self.spec['libgpg-error'].prefix]
+        return args
--- a/var/spack/repos/builtin/packages/libassuan/package.py
+++ b/var/spack/repos/builtin/packages/libassuan/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 Libassuan(AutotoolsPackage):
+    """Libassuan is a small library implementing the so-called Assuan
+       protocol."""
+
+    homepage = "https://gnupg.org/software/libassuan/index.html"
+    url = "https://gnupg.org/ftp/gcrypt/libassuan/libassuan-2.4.3.tar.bz2"
+
+    version('2.4.3', '8e01a7c72d3e5d154481230668e6eb5a')
+
+    depends_on('libgpg-error')
+
+    def configure_args(self):
+        args = ['--with-libgpp-error=%s' % self.spec['libgpg-error'].prefix]
+        return args
--- a/var/spack/repos/builtin/packages/libgcrypt/package.py
+++ b/var/spack/repos/builtin/packages/libgcrypt/package.py
@ -32,8 +32,9 @@ class Libgcrypt(AutotoolsPackage):
       key algorithms, large integer functions, random numbers and a lot
       of supporting functions. """
    homepage = "http://www.gnu.org/software/libgcrypt/"
-    url      = "http://gd.tuwien.ac.at/pub/gnupg/libgcrypt/libgcrypt-1.6.2.tar.bz2"
+    url = "https://gnupg.org/ftp/gcrypt/libgcrypt/libgcrypt-1.7.6.tar.bz2"

+    version('1.7.6', '54e180679a7ae4d090f8689ca32b654c')
    version('1.6.2', 'b54395a93cb1e57619943c082da09d5f')

    depends_on("libgpg-error")
--- a/var/spack/repos/builtin/packages/libgpg-error/package.py
+++ b/var/spack/repos/builtin/packages/libgpg-error/package.py
@ -32,7 +32,8 @@ class LibgpgError(AutotoolsPackage):
       SmartCard Daemon and possibly more in the future. """

    homepage = "https://www.gnupg.org/related_software/libgpg-error"
-    url      = "http://gd.tuwien.ac.at/pub/gnupg/libgpg-error/libgpg-error-1.18.tar.bz2"
+    url = "https://gnupg.org/ftp/gcrypt/libgpg-error/libgpg-error-1.27.tar.bz2"

+    version('1.27', '5217ef3e76a7275a2a3b569a12ddc989')
    version('1.21', 'ab0b5aba6d0a185b41d07bda804fd8b2')
    version('1.18', '12312802d2065774b787cbfc22cc04e9')
--- a/var/spack/repos/builtin/packages/libksba/package.py
+++ b/var/spack/repos/builtin/packages/libksba/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 Libksba(AutotoolsPackage):
+    """Libksba is a library to make the tasks of working with X.509
+       certificates, CMS data and related objects more easy. """
+
+    homepage = "https://gnupg.org/software/libksba/index.html"
+    url = "https://gnupg.org/ftp/gcrypt/libksba/libksba-1.3.5.tar.bz2"
+
+    version('1.3.5', '8302a3e263a7c630aa7dea7d341f07a2')
+
+    depends_on('libgpg-error')
+
+    def configure_args(self):
+        args = ['--with-libgpp-error=%s' % self.spec['libgpg-error'].prefix]
+        return args
--- a/var/spack/repos/builtin/packages/npth/package.py
+++ b/var/spack/repos/builtin/packages/npth/package.py
@ -0,0 +1,35 @@
+##############################################################################
+# 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 Npth(AutotoolsPackage):
+    """nPth is a library to provide the GNU Pth API and thus a
+       non-preemptive threads implementation."""
+
+    homepage = "https://gnupg.org/software/npth/index.html"
+    url = "https://gnupg.org/ftp/gcrypt/npth/npth-1.4.tar.bz2"
+
+    version('1.4', '76cef5542e0db6a339cf960641ed86f8')
--- a/var/spack/repos/builtin/packages/openbabel/package.py
+++ b/var/spack/repos/builtin/packages/openbabel/package.py
@ -0,0 +1,80 @@
+##############################################################################
+# 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 Openbabel(CMakePackage):
+    """Open Babel is a chemical toolbox designed to speak the many languages
+    of chemical data. It's an open, collaborative project allowing anyone to
+    search, convert, analyze, or store data from molecular modeling, chemistry,
+    solid-state materials, biochemistry, or related areas."""
+
+    homepage = "http://openbabel.org/wiki/Main_Page"
+    url      = "https://sourceforge.net/projects/openbabel/files/openbabel/2.4.1/openbabel-2.4.1.tar.gz"
+
+    version('2.4.1', 'd9defcd7830b0592fece4fe54a137b99')
+
+    variant('python', default=True, description='Build Python bindings')
+
+    extends('python', when='+python')
+
+    depends_on('python', type=('build', 'run'), when='+python')
+    depends_on('cmake@2.4.8:', type='build')
+    depends_on('pkg-config',   type='build')
+    depends_on('cairo')       # required to support PNG depiction
+    depends_on('eigen@3.0:')  # required if using the language bindings
+    depends_on('libxml2')     # required to read/write CML files, XML formats
+    depends_on('zlib')        # required to support reading gzipped files
+
+    # Needed for Python 3.6 support
+    patch('python-3.6-rtld-global.patch', when='@:2.4.1+python')
+
+    # Convert tabs to spaces. Allows unit tests to pass
+    patch('testpdbformat-tabs-to-spaces.patch', when='@:2.4.1')
+
+    def cmake_args(self):
+        spec = self.spec
+        args = []
+
+        if '+python' in spec:
+            args.extend([
+                '-DPYTHON_BINDINGS=ON',
+                '-DPYTHON_EXECUTABLE={0}'.format(spec['python'].command.path),
+            ])
+        else:
+            args.append('-DPYTHON_BINDINGS=OFF')
+
+        return args
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def check_install(self):
+        obabel = Executable(join_path(self.prefix.bin, 'obabel'))
+        obabel('-:C1=CC=CC=C1Br', '-omol')
+
+        if '+python' in self.spec:
+            # Attempt to import the Python modules
+            for module in ['openbabel', 'pybel']:
+                python('-c', 'import {0}'.format(module))
--- a/var/spack/repos/builtin/packages/openbabel/python-3.6-rtld-global.patch
+++ b/var/spack/repos/builtin/packages/openbabel/python-3.6-rtld-global.patch
@ -0,0 +1,42 @@
+The DLFCN module has been removed from python 3.6, as it is not
+documented. Same funtionality can be achive with the os module
+that makes available the os.RTLD_GLOBAL variable for dlopen()
+
+See https://github.com/openbabel/openbabel/pull/372 for the
+source of this patch. The original patch only affects the CMake
+file that SWIG uses to generate openbabel.py. This patch also
+includes changes to openbabel.py.
+
+diff -Nuar a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
+--- a/scripts/CMakeLists.txt	2017-05-17 10:02:54.408527942 -0500
+++ b/scripts/CMakeLists.txt	2017-05-17 10:04:09.701598715 -0500
+@@ -81,11 +81,8 @@
+             COMMAND ${SWIG_EXECUTABLE} -python -c++ -small -O -templatereduce -naturalvar -I${openbabel_SOURCE_DIR}/include -I${openbabel_BINARY_DIR}/include -o ${openbabel_SOURCE_DIR}/scripts/python/openbabel-python.cpp ${eigen_define} -outdir ${openbabel_SOURCE_DIR}/scripts/python ${openbabel_SOURCE_DIR}/scripts/openbabel-python.i
+               COMMAND ${CMAKE_COMMAND} -E echo "import sys" > ob.py
+               COMMAND ${CMAKE_COMMAND} -E echo "if sys.platform.find('linux'\) != -1:" >> ob.py
+-              COMMAND ${CMAKE_COMMAND} -E echo "  try:" >> ob.py
+-              COMMAND ${CMAKE_COMMAND} -E echo "    import dl" >> ob.py
+-              COMMAND ${CMAKE_COMMAND} -E echo "  except ImportError:" >> ob.py
+-              COMMAND ${CMAKE_COMMAND} -E echo "    import DLFCN as dl" >> ob.py
+-              COMMAND ${CMAKE_COMMAND} -E echo "  sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)" >> ob.py
+              COMMAND ${CMAKE_COMMAND} -E echo "  import os" >> ob.py
+              COMMAND ${CMAKE_COMMAND} -E echo "  sys.setdlopenflags(sys.getdlopenflags() | os.RTLD_GLOBAL)" >> ob.py
+               COMMAND cat ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py >> ob.py
+               COMMAND ${CMAKE_COMMAND} -E copy ob.py ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py
+               COMMAND ${CMAKE_COMMAND} -E remove ob.py
+diff -Nuar a/scripts/python/openbabel.py b/scripts/python/openbabel.py
+--- a/scripts/python/openbabel.py	2017-05-17 10:02:54.398527534 -0500
+++ b/scripts/python/openbabel.py	2017-05-17 10:04:26.705292138 -0500
+@@ -1,10 +1,7 @@
+ import sys
+ if sys.platform.find('linux') != -1:
+-  try:
+-    import dl
+-  except ImportError:
+-    import DLFCN as dl
+-  sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)
+  import os
+  sys.setdlopenflags(sys.getdlopenflags() | os.RTLD_GLOBAL)
+ # This file was automatically generated by SWIG (http://www.swig.org).
+ # Version 3.0.10
+ #
--- a/var/spack/repos/builtin/packages/openbabel/testpdbformat-tabs-to-spaces.patch
+++ b/var/spack/repos/builtin/packages/openbabel/testpdbformat-tabs-to-spaces.patch
@ -0,0 +1,47 @@
+From 08cd38485d4cf1df8802da540f3018921dbc735e Mon Sep 17 00:00:00 2001
+From: "Adam J. Stewart" <ajstewart426@gmail.com>
+Date: Wed, 17 May 2017 10:56:23 -0500
+Subject: [PATCH] Convert tabs to spaces in testpdbformat.py
+
+See https://github.com/openbabel/openbabel/pull/1568
+
+---
+ test/testpdbformat.py | 12 ++++++------
+ 1 file changed, 6 insertions(+), 6 deletions(-)
+
+diff --git a/test/testpdbformat.py b/test/testpdbformat.py
+index 40bd316..ceb8496 100644
+--- a/test/testpdbformat.py
+++ b/test/testpdbformat.py
+@@ -24,12 +24,12 @@ class TestPDBFormat(BaseTest):
+ 
+     def testInsertionCodes(self):
+         """
+-	Testing a PDB entry with insertion codes to distinguish residues
+-	upon conversion to FASTA.
+        Testing a PDB entry with insertion codes to distinguish residues
+        upon conversion to FASTA.
+         """
+         self.canFindExecutable("babel")
+ 
+-	self.entryPDBwithInsertioncodes="""ATOM    406  N   VAL L  29      58.041  17.797  48.254  1.00  0.00           N  
+        self.entryPDBwithInsertioncodes="""ATOM    406  N   VAL L  29      58.041  17.797  48.254  1.00  0.00           N  
+ ATOM    407  CA  VAL L  29      57.124  18.088  47.170  1.00  0.00           C  
+ ATOM    408  C   VAL L  29      55.739  17.571  47.538  1.00  0.00           C  
+ ATOM    409  O   VAL L  29      55.535  16.362  47.550  1.00  0.00           O  
+@@ -100,9 +100,9 @@ ATOM    473  HE1 TYR L  32      48.512  15.775  42.066  1.00  0.00           H
+ ATOM    474  HE2 TYR L  32      48.145  19.172  44.648  1.00  0.00           H  
+ ATOM    475  HH  TYR L  32      46.462  17.658  44.280  1.00  0.00           H  
+ """
+-	output, error = run_exec(self.entryPDBwithInsertioncodes,
+-				     "babel -ipdb -ofasta")
+-	self.assertEqual(output.rstrip().rsplit("\n",1)[1], "VSSSY")
+        output, error = run_exec(self.entryPDBwithInsertioncodes,
+                                     "babel -ipdb -ofasta")
+        self.assertEqual(output.rstrip().rsplit("\n",1)[1], "VSSSY")
+ 
+ if __name__ == "__main__":
+     testsuite = []
+-- 
+2.9.4
+
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@ -531,6 +531,8 @@ def setup_dependent_package(self, module, dependent_spec):
        module.site_packages_dir = join_path(dependent_spec.prefix,
                                             self.site_packages_dir)

+        self.spec.home = self.home
+
        # Make the site packages directory for extensions
        if dependent_spec.package.is_extension:
            mkdirp(module.site_packages_dir)
--- a/var/spack/repos/builtin/packages/root/package.py
+++ b/var/spack/repos/builtin/packages/root/package.py
@ -44,6 +44,7 @@ class Root(CMakePackage):
    version('6.06.06', '4308449892210c8d36e36924261fea26')
    version('6.06.04', '55a2f98dd4cea79c9c4e32407c2d6d17')
    version('6.06.02', 'e9b8b86838f65b0a78d8d02c66c2ec55')
+    version('5.34.36', '6a1ad549b3b79b10bbb1f116b49067ee')

    if sys.platform == 'darwin':
        patch('math_uint.patch', when='@6.06.02')