added a bunch of packages and added submodule

.gitignore

@@ -8,3 +8,4 @@
 /etc/spackconfig
 /share/spack/dotkit
 /share/spack/modules
+*.ropeproject

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "utils/python_recipe_parser"]
+[submodule "/lib/spack/spack/util/python_recipe_parser"]
-	path = utils/python_recipe_parser
+	path = /lib/spack/spack/util/python_recipe_parser
 	url = https://github.com/karenyyng/spack_python_package_parser

utils/python_recipe_parser

@@ -1 +0,0 @@
-Subproject commit 3158074a2d74f99aa72289dfcf093b1b0ba4474e

var/spack/packages/asciidoc/package.py

@@ -1,18 +0,0 @@
-from spack import *
-
-class Asciidoc(Package):
-    """ A presentable text document format for writing articles, UNIX man
-    pages and other small to medium sized documents."""
-    homepage = "http://asciidoc.org"
-    url      = "http://downloads.sourceforge.net/project/asciidoc/asciidoc/8.6.9/asciidoc-8.6.9.tar.gz"
-
-    version('8.6.9', 'c59018f105be8d022714b826b0be130a')
-
-    depends_on('libxml2')
-    depends_on('libxslt')
-
-    def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix)
-
-        make()
-        make("install")

var/spack/packages/boost/package.py

@@ -14,10 +14,6 @@ class Boost(Package):
     list_url = "http://sourceforge.net/projects/boost/files/boost/"
     list_depth = 2
 
-    version('1.59.0', '6aa9a5c6a4ca1016edd0ed1178e3cb87')
-    version('1.58.0', 'b8839650e61e9c1c0a89f371dd475546')
-    version('1.57.0', '1be49befbdd9a5ce9def2983ba3e7b76')
-    version('1.56.0', 'a744cf167b05d72335f27c88115f211d')
     version('1.55.0', 'd6eef4b4cacb2183f2bf265a5a03a354')
     version('1.54.0', '15cb8c0803064faef0c4ddf5bc5ca279')
     version('1.53.0', 'a00d22605d5dbcfb4c9936a9b35bc4c2')

var/spack/packages/bowtie2/bowtie2-2.5.patch

@@ -1,16 +0,0 @@
---- Makefile	2015-02-26 10:50:00.000000000 -0800
-+++ Makefile.new	2015-07-29 18:03:59.891357399 -0700
-@@ -22,10 +22,10 @@
- #
- 
- INC =
--GCC_PREFIX = $(shell dirname `which gcc`)
-+GCC_PREFIX =
- GCC_SUFFIX =
--CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
--CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
-+CC = cc 
-+CPP = c++
- CXX = $(CPP)
- HEADERS = $(wildcard *.h)
- BOWTIE_MM = 1

var/spack/packages/bowtie2/package.py

@@ -1,24 +0,0 @@
-from spack import *
-from glob import glob
-class Bowtie2(Package):
-    """Description"""
-    homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml"
-    version('2.2.5','51fa97a862d248d7ee660efc1147c75f', url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip")
-
-    patch('bowtie2-2.5.patch',when='@2.2.5', level=0)
-
-    def install(self, spec, prefix):
-        make()
-        mkdirp(prefix.bin)
-        for bow in glob("bowtie2*"):
-            install(bow, prefix.bin)
-        # install('bowtie2',prefix.bin)
-        # install('bowtie2-align-l',prefix.bin)
-        # install('bowtie2-align-s',prefix.bin)
-        # install('bowtie2-build',prefix.bin)
-        # install('bowtie2-build-l',prefix.bin)
-        # install('bowtie2-build-s',prefix.bin)
-        # install('bowtie2-inspect',prefix.bin)
-        # install('bowtie2-inspect-l',prefix.bin)
-        # install('bowtie2-inspect-s',prefix.bin)
-

var/spack/packages/cscope/package.py

@@ -1,17 +0,0 @@
-from spack import *
-
-class Cscope(Package):
-    """Cscope is a developer's tool for browsing source code."""
-    homepage = "http://http://cscope.sourceforge.net/"
-    url      = "http://downloads.sourceforge.net/project/cscope/cscope/15.8b/cscope-15.8b.tar.gz"
-
-    version('15.8b', '8f9409a238ee313a96f9f87fe0f3b176')
-
-    # Can be configured to use flex (not necessary)
-    # ./configure --with-flex
-
-    def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix)
-
-        make()
-        make("install")

var/spack/packages/czmq/package.py

@@ -1,19 +0,0 @@
-from spack import *
-
-class Czmq(Package):
-    """ A C interface to the ZMQ library """
-    homepage = "http://czmq.zeromq.org"
-    url      = "https://github.com/zeromq/czmq/archive/v3.0.2.tar.gz"
-
-    version('3.0.2', '23e9885f7ee3ce88d99d0425f52e9be1', url='https://github.com/zeromq/czmq/archive/v3.0.2.tar.gz')
-
-    depends_on('zeromq')
-
-    def install(self, spec, prefix):
-        bash = which("bash")
-        bash("./autogen.sh")
-        configure("--prefix=%s" % prefix)
-
-        make()
-        make("install")
-

var/spack/packages/docbook-xml/package.py

@@ -1,19 +0,0 @@
-import os
-import glob
-from spack import *
-
-
-class DocbookXml(Package):
-    """Docbook DTD XML files."""
-    homepage = "http://www.oasis-open.org/docbook"
-    url = "http://www.oasis-open.org/docbook/xml/4.5/docbook-xml-4.5.zip"
-
-    version('4.5', '03083e288e87a7e829e437358da7ef9e')
-
-    def install(self, spec, prefix):
-        cp = which('cp')
-
-        install_args = ['-a', '-t', prefix]
-        install_args.extend(glob.glob('*'))
-
-        cp(*install_args)

var/spack/packages/doxygen/package.py

@@ -1,25 +0,0 @@
-#------------------------------------------------------------------------------
-# Author: Justin Too <justin@doubleotoo.com>
-# Date: September 11, 2015
-#------------------------------------------------------------------------------
-
-from spack import *
-
-class Doxygen(Package):
-    """Doxygen is the de facto standard tool for generating documentation
-    from annotated C++ sources, but it also supports other popular programming
-    languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba,
-    Microsoft, and UNO/OpenOffice flavors), Fortran, VHDL, Tcl, and to some extent D..
-    """
-    homepage = "http://www.stack.nl/~dimitri/doxygen/"
-    url      = "http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.10.src.tar.gz"
-
-    version('1.8.10', '79767ccd986f12a0f949015efb5f058f')
-
-    depends_on("cmake@2.8.12:")
-
-    def install(self, spec, prefix):
-        cmake('.', *std_cmake_args)
-
-        make()
-        make("install")

var/spack/packages/eigen/package.py

@@ -0,0 +1,17 @@
+from spack import *
+
+class Eigen(Package):
+    """Eigen is a C++ template library for linear algebra: matrices, vectors,
+    numerical solvers, and related algorithms.."""
+    homepage = "http://eigen.tuxfamily.org/"
+    url      = "http://bitbucket.org/eigen/eigen/get/3.2.5.tar.gz"
+
+    version('3.2.5', '8cc513ac6ec687117acadddfcacf551b')
+
+    def install(self, spec, prefix):
+        import os 
+        os.system("mkdir ./build_dir && cd ./build_dir")
+        cmake('../', *std_cmake_args)
+
+        make()
+        make("install")

var/spack/packages/elfutils/package.py

@@ -1,26 +0,0 @@
-from spack import *
-
-class Elfutils(Package):
-    """elfutils is a collection of various binary tools such as
-    eu-objdump, eu-readelf, and other utilities that allow you to
-    inspect and manipulate ELF files. Refer to Table 5.Tools Included
-    in elfutils for Red Hat Developer for a complete list of binary
-    tools that are distributed with the Red Hat Developer Toolset
-    version of elfutils."""
-
-    homepage = "https://fedorahosted.org/elfutils/"
-
-    version('0.163',
-            git='git://git.fedorahosted.org/git/elfutils.git',
-            tag='elfutils-0.163')
-
-    provides('elf')
-
-    def install(self, spec, prefix):
-        autoreconf = which('autoreconf')
-        autoreconf('-if')
-
-        configure('--prefix=%s' % prefix, '--enable-maintainer-mode')
-        make()
-        make("install")
-

var/spack/packages/fish/package.py

@@ -1,18 +0,0 @@
-from spack import *
-
-class Fish(Package):
-    """fish is a smart and user-friendly command line shell for OS X, Linux, and
-    the rest of the family.
-    """
-
-    homepage = "http://fishshell.com/"
-    url      = "http://fishshell.com/files/2.2.0/fish-2.2.0.tar.gz"
-    list_url = homepage
-
-    version('2.2.0', 'a76339fd14ce2ec229283c53e805faac48c3e99d9e3ede9d82c0554acfc7b77a')
-
-    def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix)
-
-        make()
-        make("install")

var/spack/packages/flux/package.py

@@ -1,36 +0,0 @@
-from spack import *
-import os
-
-class Flux(Package):
-    """ A next-generation resource manager (pre-alpha) """
-
-    homepage = "https://github.com/flux-framework/flux-core"
-    url      = "https://github.com/flux-framework/flux-core"
-
-    version('master', branch='master', git='https://github.com/flux-framework/flux-core')
-
-    # Also needs autotools, but should use the system version if available
-    depends_on("zeromq@4.0.4:")
-    depends_on("czmq@2.2:")
-    depends_on("lua@5.1:5.1.99")
-    depends_on("munge")
-    depends_on("libjson-c")
-    depends_on("libxslt")
-    # TODO: This provides a catalog, hacked with environment below for now
-    depends_on("docbook-xml")
-    depends_on("asciidoc")
-    depends_on("python")
-    depends_on("py-cffi")
-
-    def install(self, spec, prefix):
-        # Bootstrap with autotools
-        bash = which('bash')
-        bash('./autogen.sh')
-
-        # Fix asciidoc dependency on xml style sheets and whatnot
-        os.environ['XML_CATALOG_FILES'] = os.path.join(spec['docbook-xml'].prefix,
-                                                       'catalog.xml')
-        # Configure, compile & install
-        configure("--prefix=" + prefix)
-        make("install", "V=1")
-

var/spack/packages/gflags/package.py

@@ -1,21 +0,0 @@
-import os
-from spack import *
-
-class Gflags(Package):
-    """The gflags package contains a C++ library that implements
-    commandline flags processing. It includes built-in support for
-    standard types such as string and the ability to define flags
-    in the source file in which they are used. Online documentation
-    available at: https://gflags.github.io/gflags/"""
-
-    homepage = "https://gflags.github.io/gflags"
-    url      = "https://github.com/gflags/gflags/archive/v2.1.2.tar.gz"
-
-    version('2.1.2', 'ac432de923f9de1e9780b5254884599f')
-
-    def install(self, spec, prefix):
-        cmake("-DCMAKE_INSTALL_PREFIX=" + prefix,
-              "-DBUILD_SHARED_LIBS=ON")
-        make()
-        make("test")
-        make("install")

var/spack/packages/ghostscript/package.py

@@ -1,17 +0,0 @@
-from spack import *
-
-class Ghostscript(Package):
-    """an interpreter for the PostScript language and for PDF. """
-    homepage = "http://ghostscript.com/"
-    url      = "http://downloads.ghostscript.com/public/ghostscript-9.16.tar.gz"
-
-    version('9.16', '829319325bbdb83f5c81379a8f86f38f')
-
-    parallel = False
-
-    def install(self, spec, prefix):
-        configure("--prefix=%s" %prefix, "--enable-shared")
-
-        make()
-        make("install")
-

var/spack/packages/glog/package.py

@@ -1,15 +0,0 @@
-import os
-from spack import *
-
-class Glog(Package):
-    """C++ implementation of the Google logging module."""
-
-    homepage = "https://github.com/google/glog"
-    url      = "https://github.com/google/glog/archive/v0.3.3.tar.gz"
-
-    version('0.3.3', 'c1f86af27bd9c73186730aa957607ed0')
-
-    def install(self, spec, prefix):
-        configure("--prefix=" + prefix)
-        make()
-        make("install")

var/spack/packages/graphviz/package.py

@@ -1,21 +1,24 @@
 from spack import *
 
 class Graphviz(Package):
-    """Graph Visualization Software"""
+    """graph visualization software."""
     homepage = "http://www.graphviz.org"
     url      = "http://www.graphviz.org/pub/graphviz/stable/SOURCES/graphviz-2.38.0.tar.gz"
 
     version('2.38.0', '5b6a829b2ac94efcd5fa3c223ed6d3ae')
+    version('2.36.0', '1f41664dba0c93109ac8b71216bf2b57')
 
-    parallel = False
+    depends_on("cairo@1.1.10")
-
+    depends_on("freetype@2.1.10")
-    depends_on("swig")
+    depends_on("fontconfig")
-    depends_on("python")
+    depends_on("zlib@1.2.3")
-    depends_on("ghostscript")
+    # depends_on("libpng@1.2.10")
+    # depends_on("expat@2.0.0")
+    # depends_on("gd@2.0.34")
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" %prefix)
+        configure('--prefix=%s' % prefix)
 
+        # FIXME: Add logic to build and install here
         make()
         make("install")
-

var/spack/packages/lapack/package.py

@@ -1,6 +1,6 @@
 from spack import *
 
-class NetlibLapack(Package):
+class Lapack(Package):
     """
     LAPACK version 3.X is a comprehensive FORTRAN library that does
     linear algebra operations including matrix inversions, least
@@ -18,16 +18,9 @@ class NetlibLapack(Package):
     version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70')
     version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4')
 
-    variant('shared', default=False, description="Build shared library version")
-
-    # virtual dependency
-    provides('lapack')
-
     # blas is a virtual dependency.
     depends_on('blas')
 
-    depends_on('cmake')
-
     # Doesn't always build correctly in parallel
     parallel = False
 
@@ -46,14 +39,7 @@ def get_blas_libs(self):
 
     def install(self, spec, prefix):
         blas_libs = ";".join(self.get_blas_libs())
-        cmake_args = [".", '-DBLAS_LIBRARIES=' + blas_libs]
+        cmake(".", '-DBLAS_LIBRARIES=' + blas_libs, *std_cmake_args)
-
-        if '+shared' in spec:
-            cmake_args.append('-DBUILD_SHARED_LIBS=ON')
-
-        cmake_args += std_cmake_args
-
-        cmake(*cmake_args)
         make()
         make("install")
 

var/spack/packages/leveldb/package.py

@@ -1,29 +0,0 @@
-import os
-import glob
-from spack import *
-
-class Leveldb(Package):
-    """LevelDB is a fast key-value storage library written at Google
-    that provides an ordered mapping from string keys to string values."""
-
-    homepage = "https://github.com/google/leveldb"
-    url      = "https://github.com/google/leveldb/archive/v1.18.tar.gz"
-
-    version('1.18', '73770de34a2a5ab34498d2e05b2b7fa0')
-
-    depends_on("snappy")
-
-    def install(self, spec, prefix):
-        make()
-
-        mkdirp(prefix.include)
-        mkdirp(prefix.lib)
-
-        cp = which('cp')
-
-        # cp --preserve=links libleveldb.* prefix/lib
-        args = glob.glob('libleveldb.*')
-        args.append(prefix + '/lib')
-        cp('--preserve=links', *args)
-
-        cp('-r', 'include/leveldb', prefix + '/include')

var/spack/packages/libdrm/package.py

@@ -11,8 +11,11 @@ class Libdrm(Package):
     version('2.4.59', '105ac7af1afcd742d402ca7b4eb168b6')
     version('2.4.33', '86e4e3debe7087d5404461e0032231c8')
 
+    depends_on("libpciaccess")
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
 
+        make("clean")
         make()
         make("install")

var/spack/packages/libelf/package.py

@@ -36,8 +36,6 @@ class Libelf(Package):
     version('0.8.13', '4136d7b4c04df68b686570afa26988ac')
     version('0.8.12', 'e21f8273d9f5f6d43a59878dc274fec7')
 
-    provides('elf')
-
     def install(self, spec, prefix):
         configure("--prefix=" + prefix,
                   "--enable-shared",

var/spack/packages/libffi/package.py

@@ -6,9 +6,9 @@ class Libffi(Package):
     to call any function specified by a call interface description at
     run time."""
     homepage = "https://sourceware.org/libffi/"
+    url      = "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz"
 
-    version('3.2.1','83b89587607e3eb65c70d361f13bab43',url = "ftp://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz")
+    version('3.1', 'f5898b29bbfd70502831a212d9249d10')
-    #version('3.1', 'f5898b29bbfd70502831a212d9249d10',url = "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz") # Has a bug $(lib64) instead of ${lib64} in libffi.pc
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)

var/spack/packages/libjson-c/package.py

@@ -1,14 +0,0 @@
-from spack import *
-
-class LibjsonC(Package):
-    """ A JSON implementation in C """
-    homepage = "https://github.com/json-c/json-c/wiki"
-    url      = "https://s3.amazonaws.com/json-c_releases/releases/json-c-0.11.tar.gz"
-
-    version('0.11', 'aa02367d2f7a830bf1e3376f77881e98')
-
-    def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix)
-
-        make()
-        make("install")

var/spack/packages/libpciaccess/package.py

@@ -1,21 +1,16 @@
 from spack import *
 
 class Libpciaccess(Package):
-    """Generic PCI access library."""
+    """Generic PCI access library"""
-
     homepage = "http://cgit.freedesktop.org/xorg/lib/libpciaccess/"
-    url      = "http://cgit.freedesktop.org/xorg/lib/libpciaccess/"
+    url      = "http://pkgs.fedoraproject.org/repo/pkgs/libpciaccess/libpciaccess-0.13.2.tar.bz2/b7c0d3afce14eedca57312a3141ec13a/libpciaccess-0.13.2.tar.bz2"
 
-    version('0.13.4', git='http://anongit.freedesktop.org/git/xorg/lib/libpciaccess.git',
+    version('0.13.2', 'b7c0d3afce14eedca57312a3141ec13a')
-            tag='libpciaccess-0.13.4')
-
-    depends_on('autoconf')
-    depends_on('libtool')
 
     def install(self, spec, prefix):
-        from subprocess import call
+        import os
-        call(["./autogen.sh"])
+        os.system("autoconf")
-        configure("--prefix=%s" % prefix)
+        configure('--prefix=%s' % prefix)
 
         make()
         make("install")