Merge pull request #1412 from adamjstewart/features/cmake

Overhaul of CMake package and compression libraries

var/spack/repos/builtin/packages/cmake/intel-c-gnu11.patch

+diff --git a/Modules/Compiler/Intel-C.cmake b/Modules/Compiler/Intel-C.cmake
+index eb9602a..edca154 100644
+--- a/Modules/Compiler/Intel-C.cmake
++++ b/Modules/Compiler/Intel-C.cmake
+@@ -16,14 +16,14 @@ endif()
+ 
+ if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 15.0.0)
+   set(CMAKE_C11_STANDARD_COMPILE_OPTION "${_std}=c11")
+-  set(CMAKE_C11_EXTENSION_COMPILE_OPTION "${_std}=c11")
++  set(CMAKE_C11_EXTENSION_COMPILE_OPTION "${_std}=gnu11")
+ endif()
+ 
+-if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 12.1)
++if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 12.0)
+   set(CMAKE_C90_STANDARD_COMPILE_OPTION "${_std}=c89")
+-  set(CMAKE_C90_EXTENSION_COMPILE_OPTION "${_std}=c89")
++  set(CMAKE_C90_EXTENSION_COMPILE_OPTION "${_std}=gnu89")
+   set(CMAKE_C99_STANDARD_COMPILE_OPTION "${_std}=c99")
+-  set(CMAKE_C99_EXTENSION_COMPILE_OPTION "${_std}=c99")
++  set(CMAKE_C99_EXTENSION_COMPILE_OPTION "${_std}=gnu99")
+ endif()
+ 
+ if(NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 12.1)

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

@@ -42,19 +42,28 @@ class Cmake(Package):
     version('3.0.2',    'db4c687a31444a929d2fdc36c4dfb95f')
     version('2.8.10.2', '097278785da7182ec0aea8769d06860c')
 
-    variant('ncurses', default=True,
-            description='Enables the build of the ncurses gui')
-    variant('openssl', default=True,
-            description="Enables CMake's OpenSSL features")
-    variant('qt', default=False, description='Enables the build of cmake-gui')
-    variant('doc', default=False,
-            description='Enables the generation of html and man page docs')
-
-    depends_on('ncurses', when='+ncurses')
-    depends_on('openssl', when='+openssl')
-    depends_on('qt', when='+qt')
+    variant('ownlibs', default=False, description='Use CMake-provided third-party libraries')
+    variant('qt',      default=False, description='Enables the build of cmake-gui')
+    variant('doc',     default=False, description='Enables the generation of html and man page documentation')
+    variant('openssl', default=True,  description="Enables CMake's OpenSSL features")
+    variant('ncurses', default=True,  description='Enables the build of the ncurses gui')
+
+    depends_on('curl',           when='~ownlibs')
+    depends_on('expat',          when='~ownlibs')
+    # depends_on('jsoncpp',        when='~ownlibs')  # circular dependency
+    depends_on('zlib',           when='~ownlibs')
+    depends_on('bzip2',          when='~ownlibs')
+    depends_on('xz',             when='~ownlibs')
+    depends_on('libarchive',     when='~ownlibs')
+    depends_on('qt',             when='+qt')
     depends_on('python@2.7.11:', when='+doc', type='build')
-    depends_on('py-sphinx', when='+doc', type='build')
+    depends_on('py-sphinx',      when='+doc', type='build')
+    depends_on('openssl',        when='+openssl')
+    depends_on('ncurses',        when='+ncurses')
+
+    # Cannot build with Intel, should be fixed in 3.6.2
+    # https://gitlab.kitware.com/cmake/cmake/issues/16226
+    patch('intel-c-gnu11.patch', when='@3.6.0:3.6.1')
 
     def url_for_version(self, version):
         """Handle CMake's version-based custom URLs."""
@@ -77,12 +86,25 @@ def install(self, spec, prefix):
         # Consistency check
         self.validate(spec)
 
-        # configure, build, install:
-        options = ['--prefix=%s' % prefix]
-        options.append('--parallel=%s' % str(make_jobs))
+        options = [
+            '--prefix={0}'.format(prefix),
+            '--parallel={0}'.format(make_jobs),
+            # jsoncpp requires CMake to build
+            # use CMake-provided library to avoid circular dependency
+            '--no-system-jsoncpp'
+        ]
+
+        if '+ownlibs' in spec:
+            # Build and link to the CMake-provided third-party libraries
+            options.append('--no-system-libs')
+        else:
+            # Build and link to the Spack-installed third-party libraries
+            options.append('--system-libs')
 
         if '+qt' in spec:
             options.append('--qt-gui')
+        else:
+            options.append('--no-qt-gui')
 
         if '+doc' in spec:
             options.append('--sphinx-html')
@@ -92,6 +114,10 @@ def install(self, spec, prefix):
             options.append('--')
             options.append('-DCMAKE_USE_OPENSSL=ON')
 
-        configure(*options)
+        bootstrap = Executable('./bootstrap')
+        bootstrap(*options)
+
         make()
+        if self.run_tests:
+            make('test')  # some tests fail, takes forever
         make('install')

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

@@ -28,15 +28,16 @@
 class Expat(Package):
     """<eXpat/> is an XML parser library written in C"""
     homepage = "http://expat.sourceforge.net/"
-    url      = "http://downloads.sourceforge.net/project/expat/expat/2.1.0/expat-2.1.0.tar.gz"
 
-    version('2.1.0', 'dd7dab7a5fea97d2a6a43f511449b7cd')
-
-    depends_on('cmake', type='build')
+    version('2.2.0', '2f47841c829facb346eb6e3fab5212e2',
+            url="http://downloads.sourceforge.net/project/expat/expat/2.2.0/expat-2.2.0.tar.bz2")
+    version('2.1.0', 'dd7dab7a5fea97d2a6a43f511449b7cd',
+            url="http://downloads.sourceforge.net/project/expat/expat/2.1.0/expat-2.1.0.tar.gz")
 
     def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
 
-        with working_dir('spack-build', create=True):
-            cmake('..', *std_cmake_args)
-            make()
-            make('install')
+        make()
+        if self.run_tests:
+            make('check')
+        make('install')

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

+##############################################################################
+# 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 Jsoncpp(Package):
+    """JsonCpp is a C++ library that allows manipulating JSON values,
+    including serialization and deserialization to and from strings.
+    It can also preserve existing comment in unserialization/serialization
+    steps, making it a convenient format to store user input files."""
+
+    homepage = "https://github.com/open-source-parsers/jsoncpp"
+    url      = "https://github.com/open-source-parsers/jsoncpp/archive/1.7.3.tar.gz"
+
+    version('1.7.3', 'aff6bfb5b81d9a28785429faa45839c5')
+
+    depends_on('cmake', type='build')
+    # depends_on('python', type='test')
+
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+            cmake('..', '-DBUILD_SHARED_LIBS=ON', *std_cmake_args)
+
+            make()
+            if self.run_tests:
+                make('test')  # Python needed to run tests
+            make('install')

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

@@ -28,14 +28,30 @@
 class Libarchive(Package):
     """libarchive: C library and command-line tools for reading and
        writing tar, cpio, zip, ISO, and other archive formats."""
+
     homepage = "http://www.libarchive.org"
     url      = "http://www.libarchive.org/downloads/libarchive-3.1.2.tar.gz"
 
+    version('3.2.1', 'afa257047d1941a565216edbf0171e72')
     version('3.1.2', 'efad5a503f66329bb9d2f4308b5de98a')
     version('3.1.1', '1f3d883daf7161a0065e42a15bbf168f')
     version('3.1.0', '095a287bb1fd687ab50c85955692bf3a')
 
+    depends_on('zlib')
+    depends_on('bzip2')
+    depends_on('lzma')
+    depends_on('lz4')
+    depends_on('xz')
+    depends_on('lzo')
+    depends_on('nettle')
+    depends_on('openssl')
+    depends_on('libxml2')
+    depends_on('expat')
+
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix)
+        configure('--prefix={0}'.format(prefix))
+
         make()
-        make("install")
+        if self.run_tests:
+            make('check')  # cannot build test suite with Intel compilers
+        make('install')

var/spack/repos/builtin/packages/libxml2/package.py

@@ -32,6 +32,7 @@ class Libxml2(Package):
     homepage = "http://xmlsoft.org"
     url      = "http://xmlsoft.org/sources/libxml2-2.9.2.tar.gz"
 
+    version('2.9.4', 'ae249165c173b1ff386ee8ad676815f5')
     version('2.9.2', '9e6a9aca9d155737868b3dc5fd82f788')
 
     variant('python', default=False, description='Enable Python support')
@@ -44,13 +45,16 @@ class Libxml2(Package):
 
     def install(self, spec, prefix):
         if '+python' in spec:
-            python_args = ["--with-python=%s" % spec['python'].prefix,
-                           "--with-python-install-dir=%s" % site_packages_dir]
+            python_args = [
+                '--with-python={0}'.format(spec['python'].prefix),
+                '--with-python-install-dir={0}'.format(site_packages_dir)
+            ]
         else:
-            python_args = ["--without-python"]
+            python_args = ['--without-python']
 
-        configure("--prefix=%s" % prefix,
-                  *python_args)
+        configure('--prefix={0}'.format(prefix), *python_args)
 
         make()
-        make("install")
+        if self.run_tests:
+            make('check')
+        make('install')

var/spack/repos/builtin/packages/lz4/package.py

+##############################################################################
+# 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 Lz4(Package):
+    """LZ4 is lossless compression algorithm, providing compression speed
+    at 400 MB/s per core, scalable with multi-cores CPU. It also features
+    an extremely fast decoder, with speed in multiple GB/s per core,
+    typically reaching RAM speed limits on multi-core systems."""
+
+    homepage = "http://cyan4973.github.io/lz4/"
+    url      = "https://github.com/Cyan4973/lz4/archive/r131.tar.gz"
+
+    version('131', '42b09fab42331da9d3fb33bd5c560de9')
+
+    # depends_on('valgrind', type='test')
+
+    def install(self, spec, prefix):
+        make()
+        if self.run_tests:
+            make('test')  # requires valgrind to be installed
+        make('install', 'PREFIX={0}'.format(prefix))

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

+##############################################################################
+# 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 Lzma(Package):
+    """LZMA Utils are legacy data compression software with high compression
+    ratio. LZMA Utils are no longer developed, although critical bugs may be
+    fixed as long as fixing them doesn't require huge changes to the code.
+
+    Users of LZMA Utils should move to XZ Utils. XZ Utils support the legacy
+    .lzma format used by LZMA Utils, and can also emulate the command line
+    tools of LZMA Utils. This should make transition from LZMA Utils to XZ
+    Utils relatively easy."""
+
+    homepage = "http://tukaani.org/lzma/"
+    url      = "http://tukaani.org/lzma/lzma-4.32.7.tar.gz"
+
+    version('4.32.7', '2a748b77a2f8c3cbc322dbd0b4c9d06a')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+
+        make()
+        if self.run_tests:
+            make('check')  # one of the tests fails for me
+        make('install')

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

@@ -45,5 +45,7 @@ def install(self, spec, prefix):
         ]
         configure(*configure_args)
         make()
-        make('check')
+        if self.run_tests:
+            make('check')
+            make('test')  # more exhaustive test
         make('install')

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

@@ -29,14 +29,18 @@ class Nettle(Package):
     """The Nettle package contains the low-level cryptographic library
     that is designed to fit easily in many contexts."""
 
-    homepage = "http://www.example.com"
+    homepage = "https://www.lysator.liu.se/~nisse/nettle/"
     url      = "http://ftp.gnu.org/gnu/nettle/nettle-2.7.1.tar.gz"
 
+    version('3.2', 'afb15b4764ebf1b4e6d06c62bd4d29e4')
     version('2.7', '2caa1bd667c35db71becb93c5d89737f')
 
     depends_on('gmp')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix)
+        configure('--prefix={0}'.format(prefix))
+
         make()
-        make("install")
+        if self.run_tests:
+            make('check')
+        make('install')

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

@@ -37,6 +37,9 @@ class Xz(Package):
     version('5.2.2', 'f90c9a0c8b259aee2234c4e0d7fd70af')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix)
+        configure('--prefix={0}'.format(prefix))
+
         make()
-        make("install")
+        if self.run_tests:
+            make('check')
+        make('install')

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

@@ -35,7 +35,9 @@ class Zlib(Package):
     version('1.2.8', '44d667c142d7cda120332623eab69f40')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix)
+        configure('--prefix={0}'.format(prefix))
 
         make()
-        make("install")
+        if self.run_tests:
+            make('test')
+        make('install')